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Revision 1.1844 - (show annotations) (download)
Fri Mar 29 23:21:39 2013 UTC (11 years, 1 month ago) by heimbach
Branch: MAIN
Changes since 1.1843: +3 -1 lines
Adding OpenAD verification experiment to isomip for shelfice package

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1843 2013/03/25 21:41:47 gforget Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 o verification/isomip, pkg/shelfic and OpenAD:
8 - add OpenAD setup to this exp and make shelfice package work with OpenAD
9 o verification/offline_exf_seaice: replace adjoint experiment.
10 o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
11 - add OpenAD setup to this exp and make ptracers package work with OpenAD
12 o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean
13 stress (when the turningAngle is non-zero) over open water to avoid
14 stripes in the EVP-solutions after many EVP-substeps. This does not change
15 the verification experiment (because turningAngle=0 in that experiment), but
16 will affect other EVP solutions with turningAngle.ne.0
17 o verification, AD & TLM output:
18 - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
19 additions and multiplications which affect results at machine truncation
20 level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
21 lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
22 (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
23 digits of matching.
24 o pkg/seaice:
25 modify lsr-algorithm so that it vectorizes AND converges by using a
26 "zebra" method: split vector loop into two with step size 2; this
27 solves a general convergence problem for the JFNK solver on a vector
28 computer. It has the potential to even improve convergence for
29 non-vector machines, but it does change the results so it is turned
30 off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
31 SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
32
33 checkpoint64e (2013/03/05)
34 o pkg/ecco and several verification experiments:
35 Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
36 from ecco package, and revert to unified routine in model/src/
37 Adjust verification experiments accordingly, especially gloal_oce_llc90
38 Should conclude long-standing work by Gael to reconsile the_main_loop with
39 ECCO and will enable OpenAD's revolve loop in ECCO setup.
40 o pkg/generic_advdiff:
41 - implement compressible flow method for multi-dim advection (similar to
42 gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
43 TAF generates many recomputations) to use it; no yet coded with implicit
44 vertical advection.
45 - change experiment advect_cs (new output) and advect_xy (same output)
46 to test compressible flow multi-dim advection.
47 o pkg/generic_advdiff:
48 - fix SOM advection for unusual cases (linear Free-Surf in r*, other
49 cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
50 o pkg/seaice:
51 - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
52 bug affects two verification experiments (lab_sea and lab_sea.hb87),
53 recover old (wrong) results by setting noSlipFac = 2. in
54 seaice_calc_strainrates.F;
55 - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
56 - add runtime parameter SEAICE_JFNKepsilon for that finite difference
57 gradient in the Jacobian times vector operation (s/r seaice_jacvec)
58 - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
59 o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
60 - new subroutines seaice_lsr_tridiagu/v
61 - introduce loop bounds i/jmin/max to be able to use a restricted
62 additive Schwarz method, but not used for now.
63 - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
64 - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
65 o OpenAD support
66 Reorganize S/R call for overall time-stepping loop to facilitate
67 OpenAD revolve loop replacement
68 (new S/R main_do_loop.F)
69 o model/src:
70 - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
71 - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
72 ADAMS_BASHFORTH2.
73 o pkg/cheapaml:
74 - add new parameter (default=F, same as before) to disable full domain
75 (including land) periodicity in X & Y dir.
76 - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
77 prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
78 into single S/R CHEAPAML_TIMESTEP.
79
80 checkpoint64d (2013/02/17)
81 o pkg/monitor (angular momentum):
82 - do not add Eta contribution to the total AM if using rigid-lid;
83 - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
84 - horizontal discretisation: compute Zonal wind contribution separately for
85 each component (instead of from cell centered averaged) and use the 4
86 grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
87 - Check that AM is conserved with linear dynamics (momAdvection=F and linear
88 FreeSurf) if using vectorInvariant momentum.
89 o model/src (horizontal grid):
90 - move initialisation of all horizontal grid arrays to null value
91 from specific horizontal grid S/R to main S/R INI_GRID;
92 - add 2 new arrays to project model C-grid velocity on to zonal direction
93 (similar to AngleCosC & -AngleSinC but at U and V point location) and
94 compute them in S/R CALC_GRID_ANGLES.
95 o pkg/seaice: replace a hard coded parameter by a runtime parameter
96 SEAICE_JFNK_tolIter
97 o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
98 preconditioner for JFNK (run LSR into the overlaps as far as possible,
99 i.e OLx/y-2, but overwrite the solution in the overlaps)
100 - extend loop range in seaice_calc_viscosity
101 - add new parameters SEAICE_OLx/y (default = OLx/y-2)
102 - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
103 - slightly modify loops in tridiagonal solver lsr-preconditioner
104 - by default remove the extra exchange in seaice_preconditioner with a
105 replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
106 - modify offline_exf_seaice so that old results without RAS are reproduced
107 for output.dyn_jfnk.txt
108 in seaice_fgmres.F (unrelated to RAS)
109 - add a cpp-flag option for a re-ordered mapping (potentially more
110 efficient), but because this changes the results, turn it off by
111 default
112 - replace the save statement by local common blocks
113 o utils/matlab:
114 - fix tile-offset in rdmnc.m when output was produced using EXCH2.
115 - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
116 instead of local script "load_cs.m".
117 o pkg/seaice:
118 - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
119 to the scalarProductMetric and the unrolling. By chance this does not
120 change the verification experiment, because of the particular domain
121 decomposition
122 o pkg/diagnostics:
123 - change default missing_value from UNSET_RL to -999.
124 o pkg/layers: improve vectorization of layers_fluxcalc.F
125 - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
126 time spent in this routine by more than a factor of 3 on an NEC-SX8
127 - step 2: replace search algorithm by a bisection algorithm found in
128 Press et al. Numerical Recipes in Fortran. This algorithm can be
129 vectorized and finds the correct bin in approx. log2(Nlayers) steps.
130 For now, use this algorithm only for TARGET_NEC_SX defined.
131 - moved the search algorithm into a separate subroutine, that is kept
132 within the same file for automatic inlining.
133 - modified catching potential errors
134 o pkg/ecco:
135 - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
136 o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
137 - modifications for ALLOW_GENTIM2D_CONTROL
138 -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
139 -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
140 -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
141 -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
142 o model/src:
143 - account for moist thermodynamics in (dry) potential temperature equation;
144 update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
145 and cpl_aim+ocn.
146 - also switch to standard compiler (gfortran, was using ifort previously)
147 for fizhi-cs experiments reference output.
148 o pkg/ctrl:
149 - 1st step toward generic time-varying control variable (2D) via CPP option
150 ALLOW_GENTIM2D_CONTROL
151 - note new namelist ctrl_nml_genarr in data.ctrl
152 o verification/global_ocean.cs32x15:
153 - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
154 thsice calling sequence and update "output.icedyn.txt" output file.
155 o pkg/ptracers:
156 - from Ryan A.: code to allow to restart a tracer at regular time interval
157 specifying a reset frequency and a reset-phase (for each tracers).
158 o pkg/thsice:
159 - implement new sequence of calls for thsice+seaice:
160 previously: ice-Dyn,ice-Advect,ice-Thermo(thsice)
161 new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
162 - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
163 in CPP_OPTIONS.h) to recover old sequence;
164 - update diagnostics for Intermediate State thsice diagnostics: now filled
165 just before advection (instead of just after advection in old sequence);
166 - update output of experiment offline_exf_seaice (standard test);
167 - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
168 by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
169 o pkg/aim_v23:
170 - use tiled array for aim_CO2 and surface wind speed for export to coupler;
171 - use standard pkg/mdsio routines to read & write CO2 pickup file;
172 - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
173 - Implement new sequence of calls for seaice advection (with thsice and
174 seaice diffusion): do ice advection after ice-Thermodynamic (previously
175 was done before); change aim_do_physics.F (split the bi,bj loops block);
176 - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
177 o pkg/thsice:
178 - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
179 where just seaice diffusion is used without seaice-dynamics.
180
181 checkpoint64c (2013/01/18)
182 o pkg/seaice:
183 - add a parameter JFNKres_tFac that can replace JFNKres_t
184 (= JFNKres_tFac*JFNKresidual before JFNK solver)
185 - add a line search option to the JFNK solver
186 - move update of u/vIce and computation of initial residual into a separate
187 routine (same file); makes the code a little easier to read (?)
188 - the line search requires computation of the residual and for some reason
189 I cannot do the update of u/vIce at the beginning of the Newton loop
190 without changing the results, so we move computation of the new residual
191 also to the end of the Newton loop, even without the line search
192 o pkg/mdsio:
193 - write missing value (corresponding to undefined array value) to meta files;
194 skip this if missing value is one (UNSET_RL would be a better value for the
195 case of undefined missing value but it's current the default missing-value);
196 Also update mdsio_read_meta.F (reading timeInterval & missing-value).
197 o pkg/exf & thsice:
198 - for diagnostics purpose, fill-up and update Qsw array (+ fill the
199 diagnostics) even when SHORTWAVE_HEATING is #undef;
200 o verification/cfc_example:
201 - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
202 illustrate how to use it).
203 o verification/offline_exf_seaice:
204 in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
205 files to only one time-record.
206 in input.thermo: narrow the 2 bands of low initial ice-concentration near
207 N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
208 snapshot output; same mcPheePiston value as in thsice with
209 surf-current=0.2m/s.
210 in input.thsice: similar set-up as in input.thermo (channel with same seaice
211 initial conditions).
212 o verification/cfc_example:
213 - update file "data" with more standard choice (default rotationPeriod,
214 exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
215 set deltaTFreeSurf to deltaTtracer) and update the output.
216 o pkg/layers:
217 - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
218 - ensure that "layers_bolus" is switched to False when useGMRedi=False.
219 o verification/offline_exf_seaice:
220 - set all {field}period to zero for constant-in-time forcing (not tested
221 anywhere else).
222 o verification/offline_exf_seaice:
223 - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
224 - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
225 o model/src:
226 - implement Finite-Volume method for (hydrostatic) presure gradient
227 from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
228 o pkg/seaice: implement EVP* by Lemieux et al. (2012).
229 - In order to be compatible with the default EVP code, this requires changing
230 the EVP code around a little; and because any small change immediately
231 breaks the lab_sea.hb87 verification experiment, the reference output is
232 updated two times (each time the remaining aggrement was only 2 digits):
233 - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
234 - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
235 The adjoint test lab_sea.evp also needed to be updated.
236 - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
237 SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
238 a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
239 explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
240 INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
241 kept obscure, because I need to test it a little more.
242 o pkg/cheapaml:
243 - fix few incorrect type (_RL/_RS) in subroutine calls.
244 o pkg/seaice:
245 - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
246 to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
247 o model/src:
248 - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
249 change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
250 experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
251 o pkg/cheapaml:
252 - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
253 update output of experiment cheapAML_box.
254 - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
255 and set them only in one place (cheapaml_readparms.F).
256 - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
257 - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
258 and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
259 o model/src/the_main_loop.F:
260 - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
261 o pkg/seaice:
262 - remove legacy branch code.
263 - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
264 o verification/*/code*/SEAICE_OPTIONS.h:
265 - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
266 SEAICE_CAP_HEFF).
267 o pkg/cheapaml:
268 - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
269 to load new forcing fields.
270 - add missing "_d 0" where it's needed; + some editing (improve indentation).
271 - remove switch to "-r8" compiler option (no longer needed) in verification
272 cheapAML_box, keep same output (small trucation error differences).
273 o verification/offline_exf_seaice:
274 - add thermodynamics only test.
275 o verification/cheapAML_box:
276 - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
277 keep same output (same 14 digits for cg2d).
278 - switch on "-r8" compiler option (some numerical values are missing
279 the "_d 0") and update output (only 6 digits for cg2d were preserved).
280
281 checkpoint64b (2012/12/24)
282 o pkg/cheapaml:
283 - remove un-used variables (Qnet,EmPmR) from pickup files.
284 - store tendency of advected variables into cheapaml pickup file
285 and fix the AB-2 restart.
286 o verification/offline_exf_seaice and lab_sea adjoint:
287 - switch to new code (#undef SEAICE_GROWTH_LEGACY).
288 - switch to 4 time steps in offline, consistent with lab_sea.
289 - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
290 - update results after change of experiment seaice.
291 o pkg/seaice:
292 - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
293 parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
294 still defined since SEAICE_multDim needs to be set to MULTDIM value (from
295 SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
296 o model/src:
297 - add run-time parameter to select CG2D solver minimum-residual solution
298 (in case of a poor convergence).
299 o pkg/seaice/seaice_lsr.F
300 - move calculation of matrix coefficients into new
301 S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
302 file; the main purpose of this change is to be able to reuse the code
303 in S/R SEAICE_PRECONDITIONER
304 - modify the computation of the residual so that the mass of sea-ice
305 is not used twice; this simplifies the calculations, but since
306 the residual is never used except when LSR_mixIniGuess.ge.4---and this is
307 not tested in testreport---this does not affect the testreport results.
308 o verification/seaice_obcs:
309 - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
310 verification/lab_sea/input.salt_plume; changes results/output.txt*
311 o model/src:
312 - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
313 o pkg/seaice:
314 - improve description of parameters in seaice_fgmres.F and start
315 cleaning up the code
316 - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
317 second argument
318 - add a metric based on grid cell area to SEAICE_SCALPROD; update
319 results of offline_exf_seaice.dyn_jfnk
320 - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
321 o pkg/aim_v23:
322 - fix an other bug in dissipation heating (grid-cell area was missing).
323 o model/src + pkg/seaice:
324 - add global (multi-tile) linear solver for pair of tri-diagonal system
325 along X and Y lines, respectively for U and V component.
326 Note: 1) MPI and cube-exchange not yet coded.
327 2) probably not accurate for poorly conditioned / large size problem.
328 - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
329 default: not compiled and not used.
330 o pkg/seaice:
331 - first attempt at a multi-threaded fgmres solver for the JFNK solver:
332 introduce bi/bj loops and use global_sum_tile_rl instead of
333 mpi_allreduce in seaice_fgmres.F
334 - improve diagnostics output for fgmres solver (seaice_fgmres.F)
335 - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
336 - add a verification experiment for JFNK in offline_exf_seaice
337 o verification:
338 - change (for now, only fwd test) offline_exf_seaice experiment:
339 use a re-entrant channel with idealized coastline (trapezoidal shape)
340 at southern boundary to explore seaice dynamics and thermodynamics
341 with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
342 secondary test (input.thsice) use thermodynamics only with SST relaxation.
343 - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
344 o pkg/exf:
345 - disable "sstExtrapol" when Nr=1
346 o verification:
347 - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
348 to test pkg/cheapaml.
349 o pkg/aim_v23 & pkg/shap_filt:
350 - fix dissipation heating (erroneous gravity multiplication factor).
351 o pkg/seaice:
352 - remove unused field pressPre from jfnk solver
353 - rename two subroutines in seaice_preconditioner.F
354 o eesupp/src:
355 - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
356 o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
357 - remove wrong parts of the rhs and the lhs (were in there
358 because I did not understand the concept of this preconditioner)
359 - add an exchange between u- and v-sweep. This increases communication
360 by a factor of two but improves the convergence of jfnk. Ideally,
361 one would like the u- and v-sweep to be independent. So far within
362 undocumented ifdefs
363 - reorganize the extra computations for printing the residuals
364 o tools/genmake2:
365 - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
366 since it's not necessary (and was preventing to use MNC in some cases).
367
368 checkpoint64a (2012/11/16)
369 o pkg/autodiff:
370 - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
371 autodiff_readparms.F no longer depends on calling order (within
372 packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
373 rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
374 and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
375 o pkg/obcs:
376 - adding tidal velocity forcing capability to obcs
377 for usage example, see verification/seaice_obcs/input.tides
378 o pkg/seaice:
379 - turn the LSR-relaxation parameters WFAU/V into runtime parameters
380 SEAICE_LSRrelaxU/V
381 - introduce runtime parameter SEAICEetaZmethod (=0 by default)
382 o pkg/aim_v23:
383 - implement heating from friction (bottom friction and stratospheric drag).
384 o pkg/shap_filt:
385 - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
386 dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
387 o model/src:
388 - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
389 time-constant addMass field from file (addMassFile);
390 - support for heating due to friction (and Kinetic Energy dissipation):
391 add option, run-time switch and 3-D field array + support code ; each pkg
392 or S/R can add heating contribution (if there is a sink of KE); the sum is
393 accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
394 o pkg/seaice:
395 - complete merge of ITD code into seaice_growth.F
396 from MITgcm_contrib/torge/itd/code/
397 no verification so far, but Torge Martin tested
398 "1-D test case and Beaufort set up;
399 deliver okay results after 1 model year."
400 - complete merge of SEAICE_SIZE.h into all relevant routines
401 - move computation of eta at Z-points into calc_viscosities
402 + introduce global field etaZ
403 + add different methods for computing etaZ, for now the old
404 method (simple averages of eta to Z-points) is hardwired
405 + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
406 seaice_preconditioner
407 - simplify computations for SEAICE_ZETA_SMOOTHREG
408 - seaice_preconditioner:
409 + replace one remaining press by pressLoc (mistake)
410 + adjust printing of residuals
411 - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
412 + add (SEAICE.h) and rename some counters (initiliased in
413 seaice_init_fixed.F)
414 + add _BEGIN/END_MASTER (myThid) around print statements
415 + print total number of iterations and failures over SEAICE_monFreq
416 interval to STDOUT
417 - move control over output-messages by fgmres to seaice_jfnk to save
418 some operations
419 - move resetting initial guess for fgmres outside of seaice_fgmres_driver
420 in order to make restarts with sol .ne. zero (fgmres with restarts)
421 (seaice_jfnk.F, seaice_fgmres.F)
422 - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
423 a serious convergence problem when open boundaries are involved
424 o pkg/ggl90: fix computation of control volumes for the case of
425 ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
426 up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
427 o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
428 o pkg/autodiff
429 - Add inAdMode switch for SEAICEuseDYNAMICS:
430 SEAICEuseDYNAMICSinAdMode
431 (extend logic in ADAUTODIFF_INADMODE_SET)
432 o pkg/seaice
433 - Step 1 of merging ice-thickness distribution (ITD) code from
434 MITgcm_contrib/torge/itd/ (author: Torge Martin)
435 The code implements concept laid out in Thorndike et al. (1975);
436 code is enabled via CPP flag SEAICE_ITD
437 nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
438 code is not complete yet!!
439 - SEAICE_SIZE.h now included in almost all seaice routines
440 o verification (using seaice):
441 - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
442 global_ocean.cs32x15.seaice ; update results.
443 - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
444 - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
445 offline_exf_seaice (previously compiling B-grid).
446 o pkg/exf:
447 - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
448 to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
449 forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
450 o pkg/layers (adjust changes from Sept 19):
451 - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
452 this allows to remove "layers_maxNum" dimension from all layers arrays.
453 o pkg/layers (adjust changes from Sept 19):
454 - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
455 - snap-shot extended to all type of layers (not just the 1rst type);
456 - remove layers variables when corresponding CPP option is undef.
457 o pkg/layers:
458 - rename pkg/layers variable and add new output (layer exist & un-weighted
459 velocity in layer)
460 o pkg/seaice:
461 - simplify (?) ocean-drag coefficent computations by using
462 the same routine in all three solvers (saves some code lines)
463 - remove global fields DRAGA and DRAGS from C-grid code and
464 declare them locally in lsr.F (the only place where they are
465 still used)
466 - update AD output of lab_sea.evp (very sensitive anyway).
467 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
468 (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
469 and SEAICEuseJFNK=.true. A few things to note:
470 - involves a FGMRES, that is parallel but very inefficient,
471 because of many scalar products (global sums) in the Gram-Schmidt
472 orthogonalization method. Needs to be replaced. Original code
473 from J.-F. Lemieux
474 - preconditioner for FGMRES is a stripped down version of LSOR
475 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
476 preconditioner. For the preconditioner, the default is set to 10.
477 - Jacobian times vector is computed with finite differences
478 - marginally related to JFNK-solver: add a smooth regularization for
479 zeta with tanh that will improve convergence (Lemieux and Tremblay,
480 2009) for any implicit solver (not implemented for EVP because EVP
481 does not need this regularization in the first place). Define
482 SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
483 o eesupp/src:
484 - check in genmake2 that intrinsic S/R flush is available.
485 - add S/R to flush IO unit (if intrinsic S/R flush is available)
486 - flush standard & error msg unit before MPI termination
487 - if debugMode, flush IO unit after printing msg
488 o pkg/ctrl:
489 - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
490 to ctrl_set_unpack_xyz.
491
492 checkpoint64 (2012/10/09)
493 o pkg/shelfice
494 - in mom_fluxform.F, mom_vecinv.F:
495 CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
496 Bug fix KappaRU -> KappaRV
497 does not change verification/isomip but may change other setups
498 (presumably constant KappaRU=KappaRV)
499 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
500 o pkg/obcs:
501 - fixed some indexing bugs in obcs_seaice_sponge.F
502 - added obcs relaxation subroutines for HSALT and HSNOW
503 - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
504 o pkg/seaice:
505 - add "multicategory" parameterization for snow in analogy to ice,
506 default is off for now.
507 o pkg/obcs:
508 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
509 see verification/seaice_obcs/input.seaiceSponge for example application.
510 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
511 index setting by master-thread. This fix multi-threads Pb in previous modifs.
512 o pkg/layers :
513 - add diagnostics to pkg/layers
514 - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
515 (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
516 o pkg/generic_advdiff/gad_implicit_r.F :
517 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
518 o pkg/seaice/seaice_growth.F:
519 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
520 o pkg/obcs:
521 - change default setting of OBCS_UVICE_OLD from defined to undef;
522 - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
523 in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
524 - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
525 - change OB null index value (OB_indexNone) to -99 ; this fix the problem
526 with Southern & Western OB at a tile edge (at least in a simple set-up).
527 o pkg/obcs:
528 - change settings of OB index in case OB coincides with tile edge (shared by
529 2 tiles), so that common OB location is registered by both tiles (instead of
530 only 1). However, for Southern and Western OB, index value = 0 is not
531 recognized as valid OB index (=default null value) and needs to be fixed.
532 - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
533 - new parameter "OB_indexNone" for null index value (for now, still zero)
534 to replace hard-coded null index value of zero.
535 o pkg/exch2:
536 - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
537 always check buffer-size (but outside the loop); move checking for valid
538 index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
539 print each tile and point connection only if |W2_printMsg|>= 2 and 3.
540 o pkg/ctrl (pack & unpack):
541 - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
542 (locally defined) for different variables (+ remove the variable-specific
543 file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
544 (to be extended to other local file names in ctrl.h).
545 o pkg/flt:
546 - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
547 o pkg/mdsio:
548 - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
549 o tools/genmake2:
550 - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
551 (added by Alistair in version 1.51 for building without make depend);
552 - remove Header files list (H_SRC_FILES) from the dependence of targets
553 ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
554 place in version 1.23): this save going through staf when unrelated header
555 file has been modified.
556 Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
557 "make depend" step, still need to do "make links" before "make adtaf".
558 o eesupp/src (+ few pkg src files) & genmake2:
559 - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
560 - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
561 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
562 upper/lower case ; account for space between "#" and undef/define)
563 o pkg/flt (with exch2):
564 - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
565 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
566
567 checkpoint63s (2012/09/05)
568 o pkg/ecco:
569 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
570 - add more relevant #ifdef ALLOW_SMOOTH ones.
571 - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
572 o pkg/ctrl:
573 - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
574 ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
575 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
576 doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
577 ctrlSmoothCorrel3D (new).
578 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
579 - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
580 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
581 controls when useAtmWind, and vice versa.
582 - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
583 - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
584 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
585 - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
586 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
587 - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
588 replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
589 o pkg/smooth:
590 - remove un-necessary includes.
591 - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
592 Those CPP options were never defined, and not necessary.
593 o model/src:
594 - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
595 - standard treatment of useSMOOTH.
596 o pkg/autodiff:
597 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
598 useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
599 o pkg/exch2:
600 - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
601 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
602 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
603 and tiles to process mapping.
604 - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
605 moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
606 rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
607 from w2_eeboot.F to w2_readparms.F.
608 o eesupp/src:
609 - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
610 ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
611 also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
612 - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
613 is defined (remove condition on usingMPI) to match cases where MPI_INIT
614 has been called.
615 - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
616 - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
617 (so that on 1 proc, get same myPid independently of usingMPI)
618 - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
619 useCubedSphereExchange with EXCH-1 (safer).
620 - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
621 o pkg/ggl90:
622 - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
623 used in ALLOW_GGL90_SMOOTH code.
624 o pkg/flt:
625 - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
626 floats at the Southern end of the domain).
627 o eesupp/inc:
628 - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
629 but not used (and not to be used) anywhere, just for documentation.
630 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
631 - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
632 a) can damage previously written records in any other multi-record files.
633 b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
634 o tools/genmake2:
635 - define variable MAKE within Makefile and use it in place of 'make';
636 - update AD_CONFIG.h (if needed) before building any of the executable
637 (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
638 and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
639 - always print usual warning comment 'this file is automatically generated'
640 from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
641 o pkg/cheapaml:
642 - updated to correspond to the code used in accepted paper (Nico Wienders).
643 o pkg/exf:
644 added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
645 ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
646 and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
647 o pkg/exf, autodiff, ctrl, ecco and seaice:
648 remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
649 o pkg/ctrl, ecco:
650 allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
651 Depending on useAtmWind, one is inactive, and the other is active (see
652 exf_getffields.F/exf_getsurfacefluxes.F).
653 o tools/genmake2:
654 - improve error msg when failing in 2nd test of check_for_broken_Ff
655 - fix option '-makefile' short-name (-mf according to genmake2 -help)
656 - source local config file "genmake_local" just after processing the genmake2
657 command arguments (previously done before processing arg).
658 o pkg/grdchk:
659 - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
660 to this routine from cost_final has been dropped in g_cost_final)
661 - improve printed information (more explicit msg, no longer using "print *,"
662 fix fcpertminus printed value).
663 o model/src:
664 - move call to COST_INIT_VARIA out of packages_init_variables.F directly
665 into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
666 this prevents getting cost-funct reset in adinitialise_varia recomputations.
667 o pkg/dic:
668 - move initialisation of "freefe" array from from dic_biotic_forcing.F to
669 fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
670 o pkg/grdchk:
671 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
672 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
673 o pkg/autodiff/ctrl/grdchk :
674 - attempt to sort out what works and what does not,
675 with regard to I/O, and to warn/stop accordingly.
676 o pkg/grdchk:
677 - attempt to fix grdchk in the case of useSingleCpuIO.
678 - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
679 statements were moved from grdchk_main.F and into
680 grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
681 - a global sum is applied to record numbers icvrec/layer
682 out of grdchk_loc so that they be passed to I/O routines.
683 o pkg/smooth:
684 - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
685 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
686 o verification/testreport:
687 - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
688 - can also use compressed (gzip) reference output file;
689 - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
690 to be easier to collect by testreport.
691 - update existing TLM output (half out-of-date by more than 3 yrs).
692 - report NETCDF & LAPACK settings (from genmake2) in output dir.
693 - report run-time in each individual summary (previously only for AD test);
694 for TLM test, add also TAF version.
695 - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
696
697 checkpoint63r (2012/08/15)
698 o tools/genmake2:
699 - fix Makefile for target ftlall (+ update files to clean after make ftlall)
700 o pkg/ecco/ecco_cost_final.F :
701 - fix fc print statements (to stdout and costfunction0000) so
702 that the printed value is always after the global sum.
703 o pkg/seaice/seaice_dynsolver.F :
704 - fix ice strength assymptote at SEAICE_area_max<1
705 (no change for the standard case of SEAICE_area_max=1)
706 o some cleaning:
707 - pkg source files: ensure that all *.F files from each pkg included the
708 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
709 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
710 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
711 includes;
712 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
713 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
714 is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
715 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
716 - update option-file CPP_OPTIONS.h of all AD experiments:
717 * no longer include PACKAGES_CONFIG.h ;
718 * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
719 * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
720 including ECCO_CPPOPTIONS.h).
721 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
722 - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
723 separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
724 not necessary accurate).
725 - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
726 pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
727 deliberately break compilation (a remainder that it needs to be customized)
728 - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
729 - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
730 - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
731 o tools/genamke2:
732 - check for lapack.
733 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
734 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
735 jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
736 from both packages.
737 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
738 - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
739 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
740 of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
741 o pkg/cost : add comments to explain special and/or untested setups.
742 o pkg/exf:
743 - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
744 (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
745 o verification/*/code_ad:
746 mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
747 - reccord when this file is included (define ECCO_CPPOPTIONS_H)
748 - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
749 allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
750 o pkg/seaice :
751 - added possibility to change ice strength/PRESS0 relationship to
752 HEFF, according to the following run time parameters
753 SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
754 SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
755 SEAICEpresH0 :: HEFF threshold for ice strength (m)
756 o pkg/ggl90 :
757 - added run time flag mxlSurfFlag to include the code that ensure
758 mixing between first and second level (previously included as a comment)
759 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
760 - add test of newly added dumpAdByRec=T option where
761 we write all records to one file per variable.
762 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
763 - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
764 to check that this code is ok with taf and compiles in adjoint.
765 o pkg/autodiff :
766 - added run time param dumpAdByRec : ad dump format switch.
767 If true then write all records to one file per variable.
768 Else write one file per record (remains the default).
769 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
770 o pkg/seaice:
771 - Added SEAICEuseTILT run time switch : if set to
772 false then omit the tilt term in seaice dynamics.
773 - Fix free drift calculation.
774 o pkg/shelfice:
775 When initializing SHELFICEDragQuadratic, set default to be
776 consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
777 but retain option to set it independently
778 (inconsistenty spotted by Veronique Dansereau)
779 o eesupp/inc:
780 - in EEPARAMS.h, add real-type constant for some frequently used simple number
781 (0,1,2,1/2), with name explicitly referring to RS/RL type.
782 o model/src:
783 - move balancing of relaxation terms to new S/R balance_relax.F.
784 o pkg/autodiff:
785 re-write active I/O high-level (control) S/R:
786 - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
787 - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
788 - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
789 MDS_READ/WRITE_FIELD); change loops to multi-threads.
790 - update and merge active_file_control_slice.flow into active_file_control.flow
791 - update the calls in lower level S/R (active_file.F, active_file_g.F and
792 active_file_ad.F) keeping the argument list and function unchanged.
793 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
794 =.TRUE.") and remove high-level (control) _loc version (not called anymore).
795 - new low-level active I/O routines, one for each type (RL/RS), for active var
796 of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
797 fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
798 right type.
799 o autodiff and RS=real*4:
800 - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
801 ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
802 - change argument type of 3-D mask argument to _RS to match type in the call
803 (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
804 o pkg/thsice:
805 - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
806 - option to correct ocean fresh-water flux for imbalance of Atmos+Land
807 fresh-water flux: uniform correction or proportional to local precip.
808 o pkg/ctrl:
809 - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
810 - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
811 ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
812 - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
813
814 checkpoint63q (2012/07/30)
815 o pkg/autodiff:
816 note about monitor and snap-shot of ad-variables:
817 a) need to apply ADEXCH before monitor or output of ad-vars to include
818 overlap contributions (was done for adjDump but missing for monitor).
819 b) since ADEXCH implies adding overlap values to interior array, machine
820 truncation error is expected when adding an ADEXCH call in the middle of
821 the time-stepping (although mathematically identical).
822 modifs:
823 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
824 declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
825 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
826 apply ADEXCH before monitor or snap-shot of ad-variables:
827 =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
828 - implement new method (copy+adexch) for snap-shot and monitor of main model
829 ad-vars (initially not used by default -> output unchanged).
830 - change default (set to 2) to use new method and update few output_adm.txt
831 with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
832 and both tutorial_tracer_adjsens tests).
833 - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
834 and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
835 o pkg/ctrl:
836 enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
837 generic control variables via
838 #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
839 Only required customization should be S/R ctrl_map_ini_genarr.F
840 (routine in repository contains example)
841 o pkg/exf:
842 - fix and refine checking of surface-relaxation setting when using EXF
843 o verification (adjoint exp):
844 - reduce length of simulation by half for experiment global_ocean.cs32x15
845 (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
846 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
847 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
848 of KE that can occur with aggressive optimization
849 + put quadratic bottom drag calculation in separated loops (only done if
850 using bottomDragQuadratic)
851 o model/src: CG2D_NSA
852 - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
853 and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
854 - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
855 change cg2d residual target to be expressed in Wunits (=> do not normalise
856 RHS ; this fix global_max Pb with TAF); update output.
857 o verification/tutorial_tracer_adjsens:
858 improve parameter consistency (and get rid of warnings):
859 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
860 - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
861 - use staggerTimeStep (for stability) in som81; use default rotation period.
862 o pkg/exch2:
863 - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
864 reset to 0 = 1 long line in X)
865 o pkg/mdsio:
866 - fix reading of dimensions from meta file for large-size domain
867 o model/src:
868 - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
869 - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
870 Cubed-Sphere Exch with CS-corners inside the domain;
871 make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
872 globalArea and to set hasWetCSCorners.
873 - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
874 metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
875 - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
876 useCDscheme and useCubedSphereExchange).
877 o pkg/seaice/seaice_growth.F :
878 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
879 for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
880 when the previous code was not correct.
881 - in all cases diagnoze the boundary condition mismatch to SIaaflux
882 - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
883 that term to QNET (essentially to set the melt/freeze water to 0degC).
884 when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
885 o verification/global_ocean.cs32x15/input.seaice :
886 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
887 - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
888 - update results (output.seaice.txt) accordingly.
889 o verification/lab_sea/input/data.seaice :
890 - remove SEAICEheatConsFix, which is now be tested
891 in global_ocean.cs32x15. The presently coded fix
892 is only consistent with real fresh water + nlfs.
893 - update results (output.txt) accordingly.
894 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
895 o AD_CONFIG.h file:
896 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
897 - remove #include "AD_CONFIG.h" from all included OPTIONS files and
898 add it explicitly in each fortran src file where it is needed.
899 motivation: header file AD_CONFIG.h is generated/modified after "make depend"
900 thus introducing potentially wrong dependency; therefore, better to include
901 it only where it's really needed, and after any other included OPTIONS file
902 (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
903 or ALLOW_TANGENTLINEAR_RUN).
904
905 checkpoint63p (2012/07/06)
906 o pkg/autodiff:
907 - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
908 - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
909 which are now read from new parameter file "data.autodiff" (inAdExact
910 previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
911 - add file "data.autodiff" in all verification/*/input_ad/ directories.
912 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
913 mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
914 o verification/tutorial_tracer_adjsens/
915 - add extra sub-verification which uses "SOM" advection scheme
916 (2nd Order-Moment Advection Scheme, Prather Limiter) with
917 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
918 and in data:
919 multiDimAdvection=.TRUE.,
920 tempAdvScheme=81,
921 saltAdvScheme=81,
922 o model/src:
923 - introduce ALLOW_BALANCE_RELAX which allow the removal
924 of the global mean of relaxation terms by setting
925 balanceThetaClimRelax and balanceSaltClimRelax
926 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
927 This case is now treated appropriately in seaice_growth.F
928 o pkg/seaice:
929 - do balanceEmPmR and balanceQnet based on the net fluxes
930 (SItflux) that enter the ocean+ice system rather than QNET
931 and EMPMR. Works best in real fresh water.
932 - SIatmFW, SIatmQnet, and SItflux computations had to be moved
933 out of the diagnotics bloc, and stored in global arrays.
934
935 checkpoint63o (2012/06/29)
936 o vertical mixing schemes:
937 - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
938 - replace computation of density (in Function STATE1, opps_calc.F) by a call
939 to S/R FIND_RHO_SCALAR
940 - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
941 and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
942 affects output (vermix.ggl90) at truncation level.
943 o testreport:
944 - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
945 (nSx,nSy) for the number of threads (from eedata.mth)
946 o model/src:
947 - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
948 related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
949 o verification/tutorial_tracer_adjsens/
950 - compile with ALLOW_CG2D_NSA
951 - run with nonlinFreeSurf=3
952 - update reference output_adm.txt
953 o tools/genmake2:
954 - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
955 refine usePROFILES switching off (only when NetCDF is not available).
956 o verification (atmospheric set-up):
957 - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
958 o pkg/profiles : refine profiles and files handling.
959 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
960 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
961 - changes to use model/src/the_main_loop.F rather than the ecco version
962 in ecco type adjoint runs.
963 o model/src:
964 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
965 - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
966 - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
967 o model/src:
968 - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
969 update output of test experiment bottom_ctrl_5x5.
970 o pkg/generic_advdiff:
971 - implement vertical bi-harmonic diffusion (for now, only for T & S and
972 only explicitly).
973 o verification/bottom_ctrl_5x5/
974 update reference output (results changed quite some time ago,
975 not sure when; but new reference results look ok in terms of grdchk)
976 o verification/1D_ocean_ice_column/
977 For verification purposes, the exact adjoint rather than an approx.
978 should be used (e.g., to comare against F.D. or TLM).
979 removed autodiff_inadmode*_ad.F routines in code_ad/
980 Update results/ accordingly.
981 o pkg/cal:
982 - change cal_getdate.F so that output date is function of input time only
983 (less ambiguous, not mixed up with input iteration number).
984 - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
985 o pkg/diagnostics:
986 - implement calendarDumps also for stats-diags
987 - implement calendarDumps also for snap-shot output (negative freq)
988 - for now, ignores calendarDumps if non-zero phase-lag.
989
990 checkpoint63n (2012/06/04)
991 o model/src:
992 - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
993 between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
994 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
995 similar to calc_r_star.F); update results of experiment internal_wave and
996 tutorial_global_oce_in_p (affected @ truncation level).
997 o pkg/shelfice:
998 - add parameterisation of advective-diffusive flux into the ice shelf
999 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
1000 - simply eps3/3a computation
1001 o eesupp:
1002 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
1003 between tiles, just fill-in edges assuming locally periodic subdomain) and
1004 add corresponding exchange subroutines (EXCH0);
1005 - new CG-solver version (_EX0) for disconnected-tiles special case.
1006 o model/src (CG-solvers):
1007 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
1008 (similar final residual output and max-Iter number as with standard version);
1009 - allows to store and use lowest-residual solution (standard & _SR versions);
1010 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
1011 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
1012 o eesup/src:
1013 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
1014 ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
1015 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
1016
1017 checkpoint63m (2012/04/27)
1018 o pkg/shelfice:
1019 - account for partical cells in surface level below ice-shelf for hydrostatic
1020 pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
1021 o ad test experiments:
1022 - update and rename to "ad_optfile.local" local AD-optfile specific to a
1023 particular adjoint verification experiment (in verification/*/code_ad/)
1024 o pkg/seaice & pkg/exf:
1025 - Part two of ECCO-CLIVAR code merges.
1026 Completes merge of seaice area relax. code.
1027 Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
1028 to be set in EXF_OPTIONS.h since this pkg controls its I/O
1029 (and avoids second CPP option in SEAICE_OPTIONS.h)
1030 - change default value of costIceStart & costIceEnd to a valid date.
1031 - add snowPrecip to HSNOW in seaice_growth
1032 o pkg/ptracers:
1033 - move ptracers summary and setup check into separated S/R ; add a check for
1034 valid PTRACERS_Iter0 value (error+stop or just warning).
1035 o pkg/cal (+ pkg/ecco):
1036 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
1037 as input; and for AD, unless both are not differentiable (e.g., k index)).
1038 o model/src:
1039 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
1040 is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
1041 temporary set to usingZCoords value (to be changed to F when using shelfice).
1042 - hydrostatic pressure: implement partial cell near the surface also for
1043 Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
1044 usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
1045 o pkg/ctrl/ctrl_init.F:
1046 - add a formal parameter to s/r ctrl_init_rec to print
1047 xx_$(ctrl_valiable)_file for easier debugging
1048 - move call of cal_* routines into the if-block where they are really
1049 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
1050 to specify a startdate
1051 o pkg/seaice:
1052 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
1053 global_ocean.cs32x15/code versions).
1054 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
1055 verification experiment global_ocean.cs32x15.seaice and update results.
1056 o pkg/exf:
1057 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
1058 (according to useExfYearlyFields).
1059 o pkg/cal:
1060 - move calendar setting & summary (previously in cal_readparams.F) into new
1061 S/R CAL_INIT_FIXED to be called later in the initialisation process, once
1062 length of the simulation is set (after SET_PARMS call); This is an attempt
1063 to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
1064 - For safety: keep a record of pkg/cal parameter settings status
1065 to allow to STOP if one pkg/cal S/R is called too early.
1066 - add a stop in all basic pkg/cal subroutines if called before setting is done.
1067 - modify cal_getdate.F: stop when nothing was returned;
1068 if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
1069 this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
1070
1071 checkpoint63l (2012/04/04)
1072 o pkg/bbl:
1073 - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
1074 update global_with_exf output.yearly.txt file.
1075 o pkg/cal:
1076 - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
1077 - remove 2 unsused and very short (1 line only) functions ;
1078 - remove unsused subroutines from AD-Diff list.
1079 o model/src:
1080 - start to implement clean wait to stop in initialization S/R (config_check.F,
1081 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
1082 o folowing PRINT_MESSAGE changes:
1083 - remove reminder multiple print to the same file (STDOUT) when multi-threads.
1084 o pkg/bbl:
1085 - modification so it can work with z*
1086 - replace deltaT with dTtracerLev(k) for asynchronous time stepping
1087 - global_with_exf/input.yearly verification; changes output.yearly.txt
1088 o eesupp/src:
1089 - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1090 writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1091 - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1092 # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1093 - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1094 - when using MPI, always set usingMPI=T ; set default accordingly and stop
1095 if not consistent.
1096 - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1097 argument is zero (in case called within single-thread section).
1098 o pkg/fizhi:
1099 clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1100 in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1101 o pkg/exch2:
1102 - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1103 activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1104 - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1105 but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1106 with bad ones coming from a not-yet-updated halo.
1107 This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1108 o pkg/frazil:
1109 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1110 http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1111 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1112 o verification/lab_sea
1113 * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1114 * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1115 * nTimeSteps 3 -> 4
1116 * changed reference output accordingly
1117 o pkg/ctrl:
1118 * fix ctrl_get_gen for xx_sst, xx_sss
1119 o pkg/fizhi:
1120 - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1121 update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1122 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1123 fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1124 clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1125 o pkg/gmredi:
1126 - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1127 o pkg/fizhi:
1128 - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1129 (old)aces open64 tuv test.
1130 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1131 o pkg/mom_vecinv:
1132 - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1133 set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1134 with non-lin free-surf).
1135 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1136 in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1137 some compilers (gfortran 4.6.0 on MacOS)
1138 o momentum:
1139 - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1140 & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1141 fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1142
1143 checkpoint63k (2012/03/17)
1144 o model/src:
1145 - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1146 flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1147 - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1148 (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1149 o model/src: solve_*diagonal.F
1150 - replace division with multiplication by inverse (similar to original version)
1151 update output of AD exp. global_ocean.90x40x15.
1152 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1153 to enable the use of the vectorized & differentiable solve_tridiagonal.F
1154 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1155 vertical advection (to get solve_tridiagonal tested in AD mode).
1156 o pkg/seaice: ECCO-CLIVAR merge:
1157 1. seaice AREA relaxation
1158 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1159 * runtime flag: SEAICE_tauAreaObsRelax
1160 2. modified global mean cost imbalance code: CPP option
1161 ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1162 o another iteration on solve_*diagonal.F
1163 Make choices independent of AUTODIFF
1164 Default will be the adjoinable vectorized version.
1165 Alternative choices are:
1166 * non-adjoinable original version with low memory footprint:
1167 #define SOLVE_DIAGONAL_LOWMEMORY
1168 * still adjoinable but does not vectorize (k as inner-most loop):
1169 #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1170 o testreport
1171 - add option to use a home made wrapper around "make"
1172 - remove MITGCM_IEEE env. variable (no longer active)
1173 o pkg/shelfice
1174 - improve computation of friction velocity for velocity dependent
1175 exchange coefficients: include velocities into SHELFICEBoundaryLayer
1176 block to average velocities vertically
1177 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1178 o Modify diagonal solvers, now three versions (upon request):
1179 #ifndef SOLVE_DIAGONAL_AUTODIFF
1180 1. default version (dating back a while ago)
1181 #else /* def SOLVE_DIAGONAL_AUTODIFF */
1182 # ifdef SOLVE_DIAGONAL_KINNER
1183 2. adjoinable version with k-innermost loop (G. Forget)
1184 # else
1185 3. adjoinable vectorized version of 2.
1186 # endif
1187 #endif /* SOLVE_DIAGONAL_AUTODIFF */
1188 All flags are currently set within routines, but could/should be moved to CPP-options.
1189 Array bounds for 1. are as before, for 2.,3. cover the entire domain
1190 (could be changed for 1. too).
1191 o verification/lab_sea (fwd):
1192 - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1193 use 7 categories (except hb87), new solve4temp params (except salt_plume),
1194 constant salinity (=4) or variable salinity (salt_plume) done through
1195 SItracer.
1196 o pkg/seaice:
1197 - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1198 - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1199 SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1200 from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1201 SEAICE_freeze got retired) but already better than previously with
1202 SEAICE_freeze=123456.7 deg.C;
1203 - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1204 (safer multi-threaded setting); always set SEAICEuseEVP;
1205 - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1206 SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1207 stop if multiple specifications for the same coeff; make sure default
1208 SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1209 o pkg/obcs:
1210 - allow to switch to upwind 1rst order advection scheme for the advective
1211 flux computation at the open-boundary; disabled for adjoint built.
1212 o pkg/ptracers:
1213 - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1214 - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1215 - add parameter to decide when to start a tracer; use internal flag to
1216 know which tracer to step-forward; switch this internal flag at the top
1217 of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1218 for adjoint built.
1219 o pkg/seaice:
1220 - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1221 - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1222 - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1223 o pkg/ecco:
1224 - fix writing of output file DiagnosCost_ClimSalt/Theta
1225 and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1226 o pkg/seaice:
1227 - add missing initialisation of COR_ICE array in dynsolver.F
1228 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1229 compiled either way, and is tested in all exps (multidim was only tested
1230 in lab_sea ad before).
1231 - cosmetic change to prepare for future addition of ITD. no change to results.
1232 no defaults change.
1233 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1234 - by lack of adequate verification experiments, I further used custom versions
1235 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1236 should be correct.
1237 - avoid recomputations in ad.
1238 o array initialisation in adjoint mode:
1239 1) pkg/mom_common/mom_calc_ke.F:
1240 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1241 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1242 part this initialisation is gone, resulting in Floating Point Exception
1243 (caught by open64 compiler with debug option).
1244 2) model/src/convective_weights.F
1245 set output convectCount over the full array range (instead of doing
1246 an update): this fix a similar issue when called within recomputation (adjoint)
1247 which could by-pass the initialisation (normally done in the caller S/R).
1248 o pkg/seaice:
1249 - final version of turbulent flux params, as agreed at MIT ice meet:
1250 SEAICE_mcPheePiston (default is ~ 0.000875)
1251 SEAICE_mcPheeTaper (default is 0.)
1252 SEAICE_frazilFrac (defualt is 1.)
1253 SEAICE_mcPheeStepFunc (default is false)
1254 - changes results at trunction error level
1255 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
1256 o added pkg/frazil:
1257 - see frazil_description.tex for details
1258 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
1259 o pkg/shelfice/shelfice_thermodynamics.F
1260 - fix exponents for velocity dependent exchange coefficients: change
1261 from 2/3(=0) to 0.66666666666666667
1262 - move computation of velocity dependent exchange coefficients into
1263 separate loop, so that it applies to both thermodynamics
1264 - move some divisions by constants out of loops
1265
1266 checkpoint63j (2012/02/16)
1267 o pkg/seaice:
1268 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
1269 - SItracer: added run time params, and allow coupling to ocn salinity.
1270 o pkg/seaice: remove (almost) all divisions by constants within loops
1271 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
1272 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
1273 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
1274 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
1275 o pkg/seaice :
1276 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
1277 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
1278 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
1279 - add permanent SItflux diag that corresponds to TFLUX but includes
1280 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
1281 - allow activation/testing of a fix for suspected missing term in
1282 ocn-ice heat budget (to be confirmed). To test this, you want to
1283 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
1284 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
1285 - no change in results, fwd or ad.
1286 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
1287 - switch to variable freezing point.
1288 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
1289 - bug fix : the sublimation term that was missing is now activated.
1290 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
1291 - bug fix : flooding sign term for SIsal0.NE.0.
1292 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
1293 o pkg/seaice:
1294 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
1295 is now the default, and the old default constant freezing point is recovered
1296 with SEAICE_tempFrz0 = -1.96,
1297 SEAICE_dTempFrz_dS = 0.,
1298 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
1299 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
1300 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
1301 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
1302 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
1303 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1304 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
1305 seaice_growth r149 for legacy branch (no results change).
1306 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1307 from I. Fenty).
1308 - results did not change except for global_ocean.cs32x15, mostly due to the
1309 switch to variable freezing point (see above item for detail).
1310 o pkg/thsice:
1311 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1312 seawater freezing in thsice_calc_thickn (not used).
1313 o pkg/seaice: turbulent flux term specification via run time params.
1314 - replace CPP switches with run time switches to facilitate testing
1315 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1316 GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1317 - added runtime parameter : SEAICEturbFluxFormula
1318 - move Mcphee constants to SEAICE_PARAMS.h
1319 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1320 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1321 remove seaice_summary call (moved to seaice_init_fixed)
1322 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1323 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1324 - seaice_summary.F : add missing report of read turbulent flux term set up
1325 and SITRACER.
1326 - seaice_check.F : check range; inform and stop if retired CPPs are used
1327 (incl. SEAICE_AGE).
1328 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1329 CPP switch, same computation as before for the different options.
1330 - change results at the truncation level.
1331 o pkg/seaice:
1332 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
1333 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
1334 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
1335 - update verification/*/input*/data.seaice:
1336 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
1337 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
1338 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
1339 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
1340 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
1341 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
1342 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
1343 difference in results only due to machine truncation.
1344 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
1345 MaykutPolySatVap; keep MIN_LWDOWN.
1346 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
1347 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
1348 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
1349 o pkg/salt_plume:
1350 - isolate saltPlumeFlux array exch into a specific S/R called from
1351 do_oceanic_phys.F
1352 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
1353 o verification:
1354 - move untested set-up to MITgcm_contrib/verification_other.
1355 o pkg/seaice:
1356 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
1357 o pkg/seaice:
1358 - seaice_solve4temp.F (keeping results unchanged):
1359 * add 2 future run-time params to select which saturation vapor pressure
1360 formula is used and how post-iteration fluxes are set.
1361 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
1362 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
1363 the linearized expression to stay consistent with tsurf finding.
1364 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
1365 can be < 0.
1366 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
1367 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
1368 conductive heat flux F_c , and add it explicitly when updating tsurf as
1369 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
1370 so that now F_ia has a consistent meaning through the entire routine.
1371 This causes differences at truncation level: update output of fwd exp.
1372 global_ocean.cs32x15.seaice.
1373 o pkg/seaice:
1374 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
1375 of arrays, sign/direction of fluxes; no effect on results.
1376 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
1377 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
1378 note: this should have been done before changing celsius2K default.
1379 - to keep results unchanged, add back old value of celsius2K in verification
1380 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
1381 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
1382 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
1383 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
1384 freezing temp is consistent with value in seaice_growth.F ; this causes
1385 differences at machine truncation level: update lab_sea AD output (3/4).
1386 o pkg/seaice:
1387 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
1388 and climsst/sss even when using seaice (to prevent calculation that might
1389 use SST on land); does not affect any verification exp.
1390 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
1391 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
1392 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
1393 over land (non-legacy code)
1394 o vectorize salt_plume package:
1395 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
1396 - this code computes plumebk everywhere (also over land), thus requires
1397 code to avoid divisions by zero and catch the case of kLev=Nr.
1398 - efficiency of salt_plume_frac is still sub-optimal
1399 o tools (genmake2):
1400 - fix makefile NAME specification (option: -makefile NAME) by adding
1401 "-f $MAKEFILE" in few places where it was missing including makedepend
1402 command (contribution from Paul).
1403
1404 checkpoint63i (2012/01/24)
1405 o model/src:
1406 - add factorized versions of some EOS code to find_rho.F,
1407 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
1408 o model/src:
1409 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
1410 - change default celsius2K from 273.16 to 273.15
1411 - to keep results unchanged, add back old value of celsius2K in verification
1412 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
1413 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
1414 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
1415 to make TAF generate vectorizable code
1416 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
1417 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
1418 have flags that do this more efficiently.
1419 o pkg/diagnostics/diagstats_calc.F
1420 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
1421 o pkg/obcs (with exch2):
1422 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
1423 and remove code (in obcs_readparms.F) which was based on EXCH of indices
1424 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
1425 o pkg/exf and seaice exp:
1426 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
1427 so that switching off area & heff advection flags does not affect results.
1428 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
1429 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
1430 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
1431 results of verification experiments: 1D_ocean_ice_column(fwd),
1432 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
1433 and offline_exf_seaice (all 4).
1434 o pkg/seaice:
1435 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
1436 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
1437 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
1438 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
1439 not multi-dim advection;
1440 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
1441 SHORTWAVE_HEATING #undef.
1442 o optim: make Makefile more robust (?)
1443 o pkg/obcs:
1444 * fix treatment of obcs_read_pickup for TAF
1445 o pkg/shelfice:
1446 * add missing initialisation of num_shifwflx
1447 * new adjoint verification exp. for isomip
1448 * change Prandtl and Schmidt numbers from generic formulations
1449 (in terms of model diffus. and visc.) to separate runtime
1450 parameters, with Holland and Jenkins (1999) default values.
1451 o pkg/exf (interpolation):
1452 - extended input field (2 rows) near the N & S poles:
1453 * fill in with the symetric value (when even Nb of data in longitude)
1454 * add average value at the poles only for scalar quantities ; for vector
1455 component interpolation, skip the averaging and keep duplicated values,
1456 unless the 2 components have same location (uvInterp=T) in which case
1457 interpolate the 2 components together using S/R EXF_INTERP_UV.
1458 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
1459 together: this allows to account properly for local orientation when
1460 averaging at N & S pole.
1461 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
1462 exf-interpolation near N & S poles. Undef by default.
1463 - add debug check/print on 1rst iter if debugLevel >=2.
1464 o pkg/exf:
1465 - change masking flags definition (no longer "parameter"), put them in
1466 common block and set them in S/R EXF_INIT_FIXED.
1467 - change recognized masking flag from s,u,v to c,w,s since the mask
1468 to use (maskC,W,S) depends on position on model grid and has little to
1469 do with scalar/vector difference; fix masking if using P-coordinates.
1470 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
1471 and update results of exp. global_with_exf (x2).
1472 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
1473 o pkg/obcs
1474 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
1475 o pkg/exf (interpolation):
1476 - assume periodicity in X only if input field cover full longitude range.
1477 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
1478 and should vectorise).
1479 - fix input lat of the 2 added row (in case we provide N.pole data).
1480
1481 checkpoint63h (2011/12/30)
1482 o pkg/seaice:
1483 - change declaration of UVM from _RL to _RS in order to get B-grid
1484 uIce,vIce monitor when _RS = real*4
1485 o pkg/offline:
1486 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
1487 - compute vertical velocity if not read from file (switch on exactConserv
1488 & staggerTimeStep);
1489 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
1490 o verification:
1491 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
1492 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1493 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1494 - update output of exp. global_ocean.cs32x15.viscA4 after changing
1495 grid-file angles (used here for coriolis-3d);
1496 - remove (or gzip) few files not needed to run fizhi-cs experiments.
1497 o pkg/exf (vector interpolation):
1498 - rotate vector component toward local grid-axis orientation using grid-angles
1499 (stored in GRID.h) instead of locally computed rotation angle; keep old code
1500 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1501 o pkg/seaice:
1502 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1503 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1504 o pkg/PKG_OPTIONS.h files:
1505 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1506 outside of the #ifdef ALLOW_THISPKG / #endif block.
1507 - update verification/*/code/PKG_OPTIONS.h files.
1508 o add a verification experiment (offline_exf_seaice/input.seaice) that test
1509 the B-grid LSOR solver
1510 o pkg/seaice: sort out emissivity and long wave radiation step 2:
1511 - add emissivity for snow and ice as new run-time parameters
1512 (unfortunately) that default to the corresponding exf values; this
1513 changes results in most verification experiments so that for backward
1514 compatibility these parameter have to be set explicitly to inconsistent
1515 values (ugly);
1516 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1517 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1518 until we agree how to handle this bug properly
1519 o pkg/exf (interpolation):
1520 - add a set of run-time param ({inputfield}_interpMethod), one for
1521 each interpolated input field, to select the interpolation method
1522 with a value of zero switching off the interpolation;
1523 - print interpolation parameters to standard output;
1524 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1525 (to use instead runoff_interpMethod=0 in data.exf).
1526 - simplify default setting of interpolation parameters (for all fields,
1527 set position to match model grid cell-center position, leading to trivial
1528 interpolation in case of regular Lat-Lon grid) and fix for the case of
1529 non-uniform delY.
1530 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1531 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1532 this factor is absolutely required, because the lw exitance (= out-going
1533 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1534 where the reflectivity rho = 1-emissivity for conservation reasons. Once
1535 this is established, we can remove the CPP-Flag (if we want to).
1536 o pkg/seaice:
1537 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1538 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1539 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1540 what the name implies (and not emissivity*BoltzmannConstant), this means
1541 the old default value of 5.5e-8 now means
1542 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1543 S/R exf_readparms
1544 - FV-discretization of the B-grid LSOR solver, turn on with
1545 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1546 of the calling routine dynsolver, so that B and C-grid code look a
1547 little more alike.
1548 - fix index bugs in ostres.F (B-grid code)
1549 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1550 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1551 default for SEAICE_emissivity, if useEXF; requires setting a wrong
1552 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1553 backward compatiblity
1554 o model/src: use sigmaR in calc_ivdc
1555
1556 checkpoint63g (2011/12/16)
1557 o pkg/seaice/seaice_growth.F:
1558 fix heat conservation of the coupled ocean-seaice system.
1559 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1560 solid vs liquid water treatment is resolved via QNET.
1561 o pkg/seaice/seaice_growth.F:
1562 add missing term for sublimation in saltFlux, which was breaking conservation.
1563 o pkg/seaice/seaice_model.F:
1564 Remove this patholigical case treatment in evolution branch,
1565 where it is un-necessary and breaks conservation.
1566 Update global_ocean.cs32x15/results accordingly for
1567 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1568 o model/src:
1569 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1570 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1571 o pkg/obcs:
1572 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1573 tendency for temperature and salinity that is then applied to update
1574 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1575 horizontal advection and diffusion contributions on the boundary (in
1576 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1577 removing the mask in S/R timestep_tracer. The advantage of this approach is
1578 that the updated tracer values include contributions from the surface
1579 forcing and vertical diffusion.
1580 This modification changes exp4.stevens because of vertical diffusion.
1581 o model/src:
1582 change non-curvilinear grid setting to also work with exch2 + blank tiles:
1583 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1584 face dimensions.
1585 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1586 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1587 and INI_SPHERICAL_POLAR_GRID.
1588 change test-experiment global_ocean.90x40x15:
1589 - split the domain in many more tiles (9x4 tiles of 10x10 each);
1590 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1591 - update results of both test (std & dwnslp).
1592 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1593 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1594 o model/src:
1595 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1596 and fix initialisation when using sigma-coords.
1597 o model/src:
1598 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
1599 to their current value at the beginning of forward_step.F": add a new run-time
1600 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
1601 - set doResetHFactors=T in the following test exp:
1602 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
1603 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
1604 and tutorial_global_oce_in_p (nonLinFS in p)
1605 o pkg/ecco
1606 - added IES cost term
1607 o verification/advect_xz
1608 - scale down the depth by 1/100 (from 200 km to just 2.km)
1609 - add secondary test using divergent flow, r-star and implicit vertical advection.
1610 - add note (check_conserve_TS.txt) and matlab script to check global
1611 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
1612 o pkg/rbcs:
1613 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
1614 o pkg/obcs (Stevens BCs):
1615 - fix various problems in the phase speed computations of the Stevens
1616 boundary conditions:
1617 - sign error for western and southern boundaries,
1618 - time tendencies were underestimated by factor of dTracerLev and some just
1619 zero (for multidim advection schemes) -> now estimate time tendencies
1620 from difference between previous (n) time level and the one before (n-1);
1621 this requires storing a field per tracer per boundary, also in the pickup
1622 files.
1623 - replace deltaTmom in cflMer/Zon computation with dTracerLev
1624 - set default phase velocity to cflMer/Zon
1625 - update verification experiment exp4.stevens
1626 o pkg/generic_advdiff (implicit_r):
1627 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
1628 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
1629 - fix implicit vertical diffusion or advection with NonLin FreeSurf
1630 (was using current recip_hFacC instead of future recip_hFacC): set future
1631 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
1632 solver S/R ;
1633 - fill diagnostics of vertical advective fluxes (computed from tendency)
1634 when using implicit vert. advection;
1635 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
1636 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
1637 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
1638 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
1639 o pkg/diagnostics:
1640 - add diags for T & S tendency which goes through Adams-Bashforth.
1641
1642 checkpoint63f (2011/11/30)
1643 o pkg/obcs/obcs_calc_stevens.F:
1644 - join some loops to reduce number of if-statements
1645 - fix a bug in code for northern and southern boundaries.
1646 o pkg/seaice/seaice_init_varia.F
1647 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
1648 caused zero ice-velocities for the B-grid code
1649 o pkg/seaice/seaice_init_fixed.F
1650 - fix a bug in the initialisation of the second metric terms
1651 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
1652 - this affects all seaice configurations with useCurviLinearGrid = .true.
1653 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
1654 = .true. (default)
1655 - the only verification experiment affected is global_ocean.cs32x15:
1656 icedyn, seaice, and seaice_dynmix (AD)
1657 o pkg/thsice/thsice_diagnostics_state.F
1658 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
1659 not contain garbage that can lead to surprises in diagstats_calc.F
1660 o model/src:
1661 - move bi,bj loops inside INTEGR_CONTINUITY ;
1662 - call INTEGR_CONTINUITY directly from forward_step.F
1663 (previously called from momentum_correction_step.F)
1664 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
1665 forward_step.F and pkg/ecco/the_main_loop.F
1666 o model/src/do_oceanic_phys.F:
1667 - reset addMass to zero only if useICEFRONT ;
1668 - separated k-loop for rhoInSitu calculation ;
1669 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
1670 and at constant T,S (= WdRHOdP);
1671 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
1672 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
1673 transport of locally-referenced potential density);
1674 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
1675 o gluemnc:
1676 - replace ncrcat with ncks when adding variables to *.glob.nc
1677 - change the way variables without record dimensions are handled so that
1678 files that have variables with and without record variables can be glued:
1679 add a record dimension with a new unique name to be able to differentiate
1680 between variable with and without a-prior record dimensions. Remove
1681 this record dimension before adding the variable to the *.glob.nc file.
1682 This procedure automatically works also for grid.*.nc files that do not
1683 have any record dimension.
1684 o verification/cpl_aim+ocn:
1685 - generate new reference output on baudelaire (gfortran, mpich2) (previously
1686 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
1687 o pkg/obcs/obcs_calc_stevens.F:
1688 - add code for northern and southern boundaries.
1689 - reorder some loops to save some operations and so that drFBar can be scalar
1690 o model/src:
1691 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
1692 truncation) and add diagnostics for Adams-Bashforth tendency increment.
1693 - update test-exp. AD output:
1694 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
1695 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
1696 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
1697 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
1698 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
1699 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
1700 tutorial_plume_on_slope.
1701 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
1702 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
1703 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
1704 does not even come with an F77 compiler anymore, this should not be
1705 a limitation
1706
1707 checkpoint63e (2011/11/06)
1708 o pkg/seaice adjoint of LSR:
1709 - substantially rework STORE dirs.
1710 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
1711 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
1712 and only perform SOLV_MAX_FIXED adjoint iters.
1713 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
1714 always goes to same record, meaning that the last forward field will be
1715 the one used in the adjoint - an approximation.
1716 - now produces non-zero LSR-related gradients, and acceptable gradients for
1717 An's zonal (x-z) test case (to be checked in)
1718 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
1719 (but these are screwed up by the thermodynamics in the first place);
1720 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
1721 output_adm.txt also reflects changes to seaice_lsr
1722 - global_ocean.cs32x15:
1723 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
1724 (output_adm.seaice.txt was updated)
1725 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
1726 (output_adm.seaice_dynmix.txt)
1727 o test-exp. exp4+stevens:
1728 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
1729 o pkg/seaice (lsr solver):
1730 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
1731 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
1732 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
1733 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
1734 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1735 - compute (with new S/R) and print initial (+ free-driff sol. if available)
1736 and final residual of linearised system.
1737 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1738 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1739 o pkg/obcs: Stevens BCs (still only for east and west)
1740 - fix Stevens BCs by using intermediate velocities of previous
1741 time step as "baroclinic" contribution rather velocity of one grid cell
1742 inside the boundaries; more consistent but makes the entire treatment
1743 more complicated, requires new pickup files and two new S/Rs:
1744 obcs_copy_uv_n and obcs_save_uv_n
1745 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1746 (undefined by default)
1747 - silently move computation of some grid factors into separate loops to
1748 save some recomputations
1749 - add a hack for non-linear free surface
1750 - add a verification experiment to exp4 that tests this code
1751 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1752
1753 checkpoint63d (2011/10/25)
1754 o pkg/obcs + seaice-dynamics:
1755 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1756 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1757 values (consistent with an implicit method).
1758 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1759 return to older implementation (same results as before); note that none of
1760 the "experimental" OBCS_SEAICE options are implemented in the new version.
1761 - switch test exp. seaice_obcs to use new version (update output).
1762 o pkg/seaice:
1763 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1764 - add parenthesis in Water-Ice drag calculations (evp & lsr);
1765 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1766 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1767 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1768 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1769 o pkg/layers:
1770 - Include potential density as new coordinate (Thanks to David Munday)
1771 o pkg/dic:
1772 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1773 carbonate computation/output to CALC_PCO2_APPROX
1774 o pkg/generic_advdiff
1775 - make TAF generate code that vectorizes:
1776 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1777 o model/src:
1778 - improve vectorization also for adjoint code of
1779 solve_tridiagonal and solve_pentadiagonal. As this requires up to
1780 5 new 3D-fields, this code is only turned on for the combination of
1781 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1782 for singular matrix check (only for TARGET_NEC_SX).
1783 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1784 ALLOW_AUTODIFF. This flag now needs to be set outside of
1785 solve_tri/pentadiagonal.F
1786 o pkg/exf:
1787 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1788 optional namelist EXF_NML_OBCS).
1789 - add many debug-print (to trace down where pkg/cal error msg comes from)
1790 o pkg/mom_vecinv/mom_vi_hdissip.F
1791 - rearrange loops so that vectorization is improved and in particular
1792 the adjoint routine vectorizes. The code is a little longer now, but I
1793 think easier to read.
1794 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1795 o pkg/seaice:
1796 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1797 o pkg/exch2:
1798 - alternative code (without tile x tile matrix) for cumulated (global) sum;
1799 used as default; keep using matrix version in adjustment.cs-32x32x1.
1800 o tools/build_options:
1801 - after merging some MPI and/or multi-threads specific optfiles so that
1802 the modified default optfile support both built (using genmake2 -mpi
1803 for the MPI built, using genmake2 -omp for OpenMP built),
1804 move now obsolete optfiles to tools/build_options/unsupported/
1805 (add copy of email sent to support list in doc/optfiles_changes.txt)
1806
1807 checkpoint63c (2011/09/28)
1808 o pkg/ebm:
1809 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1810 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1811 o pkg/seaice (SItracer pickup)
1812 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1813 To be done:
1814 - thorough testing of missing fields in S/R seaice_read_pickup
1815 - thorough matching between generic tracers and specific fields used
1816 (e.g. volume-weighted age, area-weighted age, salinity, ...)
1817 o pkg/grdchk:
1818 - all procs calculate and print finite-difference gradient (for testreport)
1819 - change description output used by testreport;
1820 - AD testing: also compare and report Finite-difference gradient;
1821 => update all output_adm*.txt
1822 o test exp. global_ocean_ebm:
1823 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1824 and turn on exactConserve; update (fwd) output.
1825 o pkg/seaice (LSR):
1826 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1827 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1828 * identical results with non-CS topology (but save up to half of EXCH calls)
1829 * no much changes in cs-32 verification tests since no ice at face edges
1830 (differences due to convergence criteria, since nb of iterations changed)
1831 * expect some differences on lat-lon-cap grid.
1832 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1833 o pkg/exch2:
1834 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1835 many tiles); until alternative coding is added, just add a stop.
1836 o pkg/kpp:
1837 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1838 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1839 o optfiles:
1840 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1841 into corresponding standard one, which now support different build:
1842 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1843 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1844 o pkg/obcs (seaice):
1845 - add missing EXCH for uIce,vIce after applying OBCS;
1846 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1847 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1848 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1849 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1850 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1851 and eedata.mth for MPI and mutlti-threaded testing.
1852 o pkg/flt:
1853 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1854 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1855 - fix pickup and trajectories + profiles output with multi-threads;
1856 - add parameter to select group of fields to write along trajectory and
1857 profile (default unchanged);
1858 - only call PORT_RAND* function when flt_noise <> 0;
1859 - add multi-threaded test for verification exp. flt_example.
1860 o eesupp/src:
1861 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1862 - USE_OMP_THREADING: check that number of threads (from eedata) matches
1863 actual number (from env.var. setting).
1864 o pkg/ebm:
1865 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1866 - add multi-threaded test for verification exp. global_ocean_ebm
1867
1868 checkpoint63b (2011/08/29)
1869 o pkg/ebm:
1870 - fix sign of runoff;
1871 - update directly forcing fields (Qnet,EmPmR) to use standard
1872 external_forcing_surf.F (remove ebm_forcing_surf.F);
1873 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1874 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1875 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1876 - update global_ocean_ebm parameters file data and update output (fwd+ad).
1877 o verification/matrix_example:
1878 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1879 MPI and mutlti-threaded testing.
1880 o pkg/matrix:
1881 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1882 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1883 - fix for multi-threaded (remove DATA statement);
1884 - use standard DIFFERENT_MULTIPLE function;
1885 - add MATRIX_OPTIONS.h
1886 o verification/matrix_example:
1887 To allow to split the domain in several tiles, change the domain size
1888 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1889 Western side) of land points.
1890 o (*_)write_pickup:
1891 - fix few bugs in mypackage_read/write_pickup.F
1892 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1893 array of length 1 (was caught by compiler syntax-check).
1894 o pkg/diagnostics (velocity potential solver):
1895 - fix initialisation of main diagonal matrix (for overlap values)
1896 o tools/build_options:
1897 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1898 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1899 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1900 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1901 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1902 and use "-devel" testreport option for standard testing on baudelaire.
1903 o pkg/grdchk:
1904 - Assume that all gradient-check position are within the same tile
1905 corresponding to global indices (iGloTile,jGloTile) and that
1906 positions (i,j indices or nbeg) are local to this tile;
1907 - set tile local-indices and proc. number according to tile global-indices;
1908 - remove grdchkwhichproc from namelist (retired param);
1909 - send adjoint gradient to all procs so that all procs print it to STDOUT;
1910 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1911 o adding package bbl (Bottom Boundary Layer)
1912 description in MITgcm/pkg/bbl/bbl_description.tex
1913 example/test experiment in MITgcm_contrib/bbl
1914 o adjoint verifications
1915 - changed 5 experiments to multi-tiles
1916 * global_ocean.90x40x15
1917 * obcs_ctrl
1918 * offline_exf_seaice
1919 * tutorial_dic_adjoffline
1920 * tutorial_tracer_adjsens
1921 changed reference output for those that crossed tile boundaries
1922 (changed choices of gradient check positions)
1923 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1924 - temporary bug fix in grdchk_loc.F for obcs
1925 o genmake2 & testreport
1926 - add target "obj" (just for OBJFILES files) to Makefile;
1927 - add option to specify FEXTRAFLAGS on command line.
1928 o pkg/mypackage:
1929 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1930
1931 checkpoint63a (2011/08/02)
1932 o pkg/diagnostics (velocity potential):
1933 - fix velocity-potential calculation when using OBCS: balance net inflow
1934 at each level (new S/R OBCS_DIAG_BALANCE).
1935 - fix some of the problems with OBCS in stream-function calculation.
1936 o pkg/exf/exf_readparms.F
1937 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1938 EXF_NML_OBCS) more consistent, so that you need not have these lists
1939 in data.exf when they are not used.
1940 o optim/optim_readdata.F:
1941 - add some output about obcs variables that might help debugging
1942 - add a check about nvarlength
1943 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1944 o pkg/diagnostics (velocity potential):
1945 - fix mask for OBCS (still problems in stream-function with OBCS);
1946 - add specific parameter (default = main code CG2D params) for solver;
1947 - in case of poor convergence, use solution corresponding to lowest residual.
1948 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1949 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1950 and should be avoided where possible.
1951 o model/src (rStar):
1952 - include r* effect on reference-state (PhiRef) in totPhiHyd
1953 (so that it's really the potential anomaly at the cell center);
1954 affect solution only if z* with full pressure in EOS.
1955 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1956 update output (because of z* in totPhiHyd and viscA4 changes);
1957 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1958 @ constant r) until interpolation at constant r is implemented.
1959 o pkg/diagnostics
1960 - fix RCENTER diagnostics in case cell center is not at interface middle
1961 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1962 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1963 that THETA and SALT are "conservative temperature" and "absolute
1964 salinity"
1965 o pkg/ctrl
1966 - fix computation of endrec in s/r ctrl_init_rec
1967 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1968 o pkg/seaice/seaice_growth.F
1969 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1970 remove then obsolete STORE directives
1971 - fix STORE directives for tice and tices, so that only the
1972 appropriate part of the fields are stored (and not the entire
1973 field); update global_ocean.cs32x15.seaice AD output.
1974 - cosmetic changes: adjust CPP flags and indentation for better
1975 legibilty
1976 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1977 Chris Wilson)
1978 o pkg/gmredi:
1979 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1980 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1981
1982 checkpoint63 (2011/07/11)
1983 o pkg/exch2:
1984 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1985 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1986 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1987 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1988 o pkg/diagnostics:
1989 - deal with pairs of post-processed diags which are computed together; in
1990 particular, re-order list of diags within 1 file to save 2nd computation.
1991 - add S/R to compute velocity stream-function (called after velocity-potential
1992 calculation) from divergence free transport -> new diagnostics "PsiVEL".
1993 - add parameter to select grid-point location where PsiVEL == 0.
1994 o eesupp/src:
1995 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1996 (specific S/R needed with exch2 topology - for now, just print an error msg)
1997 o pkg/shelfice
1998 - Implement friction velocity-dependent transfer coefficients following
1999 Holland and Jenkins, JPO, 1999
2000 Original code by M. Losch with small modifs.
2001 Enable with CPP option SHI_ALLOW_GAMMAFRICT
2002 and runtime flag SHELFICEuseGammaFrict
2003 o verification lab_sea & global_ocean.cs32x15:
2004 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
2005 does not miss some dependencies (but is slower) and also works with many files
2006 (default makedepend limitation for AD built).
2007 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
2008 o pkg/diagnostics:
2009 - add run-time parameter "useMissingValue" (def=False) to fill land-point
2010 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
2011 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
2012 - Extend the use of "missing_value" setting from data.diagnostics for the case
2013 of counter-diagnostics (where fraction-weight is zero). This applies both to
2014 MNC and MDS output files.
2015 o pkg/seaice/seaice_growth.F:
2016 - add 'a priori' cap of latent heat flux based on actual mass considerations
2017 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
2018 non-legacy seaice_solve4temp.
2019 - add diagnostic of the residual sublimation freshwater flux (the freshwater
2020 flux taken from the ocean if the total actual latent heat fluxes exceed
2021 the maximum)
2022 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
2023 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
2024 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
2025 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
2026 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
2027 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
2028 o verification 1D_ocean_ice_column:
2029 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
2030 update results
2031 o pkg/diagnostics:
2032 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
2033 which are not filled-up but computed from other diags ; In this case, the mate
2034 diag points to the primary (filled-up) diag to used for post processing.
2035 - Update Velocity-potential computation using post-processed diag framework.
2036 ==> Change the ordering of fields and time-periods in MDS output file
2037 when using periodic averaging: now writes one time record with the full set
2038 of fields for this time period, then the next time reccord (it used to be
2039 one field with the full set of time records then the next field).
2040 Note: this is now similar to NetCDF (MNC) output file. <==
2041
2042 checkpoint62z (2011/06/21)
2043 o adjoint monitor:
2044 - Add adjoint monitor output for packages exf, seaice
2045 and update relevant testreport output
2046 o pkg/seaice:
2047 - re-order diags inits so that they appear in order in available_diagnostics.log
2048 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
2049 area/heff/hsnow preceeding thermodynamic growth/melt.
2050 - modified diag: SIdA; output actual effect, as the description states.
2051 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
2052 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
2053 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
2054 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
2055 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
2056 - added diagnostics for seaice generic tracers (SItr*).
2057 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
2058 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
2059 I. Fenty: 18-Jun-2011:
2060 Minor changes to seaice package:
2061 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
2062 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
2063 - Differentiated "regularization variables" from "floor variables"
2064 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
2065 * hiceMin became SEAICE_hice_reg (old hiceMin)
2066 (with _reg meaning regularization variable)
2067 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
2068 so as to ensure energy conservation when going between phases
2069 - A22 was not used anywhere
2070 2) Changed regularization procedure for heffActual and hsnowActual to ensure
2071 well-boundedness and smooth adjoint in seaice_growth.F
2072 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
2073 because the old regularization always set heffActual >= 0.05 cm
2074 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
2075 on AREA when HEFF > 0.
2076 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
2077 requiring that DISABLE_AREA_FLOOR *not* be defined
2078 Affected verifications:
2079 - 1D_ocean_ice_column (output.txt output_adm.txt)
2080 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
2081 o pkg/diagnostics:
2082 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
2083 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
2084 (was _RL, now integer) with option = 0 to retrieve all levels.
2085 - add pieces of code to compute velocity potential at each level (new diagnostics
2086 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
2087 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
2088 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
2089 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
2090 and in diagnostics_fract_fill.F (do not need a valid pointer for the
2091 diagnostics counter-mate); check that definition of counter-diagnostic
2092 includes a valid counter-mate (in diagnostics_set_levels.F).
2093 o model/src (rStar):
2094 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
2095 affect solution only if z* with full pressure in EOS;
2096 update output of test-exp global_ocean.90x40x15.
2097 o pkg/seaice:
2098 - introduce siEps=1e-5 parameter
2099 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
2100 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
2101 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
2102 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
2103 as well as ice cover age and ridging index (attached to AREA).
2104 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
2105 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
2106 Up to SItrMaxNum=3 tracers can be used simultaneously.
2107 o pkg/salt_plume:
2108 -introduce SPsalFRAC run time parameter that sets the fraction of the
2109 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
2110 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
2111 o model debug options:
2112 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
2113 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
2114 - Refine debug-msg printing selection (3 new levels):
2115 debugMode : controls printing of debug messages (sequence of S/R calls).
2116 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
2117 debLevZero = 0 ; /* level of disabled aux. msg printing */
2118 debLevA = 1 ; /* level of minimum aux. msg printing */
2119 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
2120 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
2121 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
2122 debLevE = 5 ; /* level of extensive debug printing */
2123 New debugLevel default: with default debugMode value (=F),
2124 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
2125 and if debugMode=T, default debugLevel = 4 (debLevD).
2126 Relation with previous settings:
2127 debLevB (=2) corresponds to former debLevA (=1)
2128 debLevD (=4) corresponds to former debLevB (=2)
2129 Note:
2130 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
2131 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
2132 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
2133 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
2134 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
2135 o pkg/obcs:
2136 - change OBCSfixTopo default from True to False (should not change the results);
2137 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
2138 o pkg/thsice:
2139 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
2140 2nd layer seaice sublimation (unlikely to happen)
2141 - use Interior mask for OBCS in thsice_advection.F (similar to what is
2142 done in gad_advection & seaice_advection).
2143 o adjoint:
2144 bug fix spotted by Gael Forget:
2145 seaice_advection and thsice_advection still had
2146 legacy CPP options to avoid CS corner updates for adjoint
2147 o pkg/seaice:
2148 => Change some of the defaults (2011/05/29):
2149 - change SEAICEuseFluxForm default (from False to True)
2150 - change DIFF1 default (from 0.004 m/s to 0. m/s)
2151 And print warnings if DIFF1 is not set in data.seaice and centered
2152 avection scheme is used without any diffusion.
2153 also:
2154 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
2155 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
2156 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
2157 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
2158 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
2159 update results of test exp.:
2160 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
2161 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
2162 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
2163 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
2164 seaice_obcs: output (SEAICEuseFluxForm=T)
2165 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
2166 for standard fwd & AD lab_sea tests (to keep the same output).
2167 o pkg/seaice/seaice_growth.F:
2168 - use Ian Fenty's capping formulas for actual ice
2169 thickness thoughout EVOLUTION branch.
2170 - put treatment pathological case #2) in CPP brackets
2171 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
2172 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
2173 o pkg/seaice:
2174 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
2175 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
2176 also pass fac as a param, which can be 1. (to update the tendency
2177 field) or the time step (to update the field itself).
2178 - seaice_advdiff.F: for multidim, call seaice_diffusion with
2179 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
2180 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
2181 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
2182 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
2183 o pkg/seaice:
2184 diffusion with centered advection scheme (diffus.F & advect.F):
2185 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
2186 to just compute the laplacian of input-field.
2187 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
2188 - fix flux-form version in diffus.F to conserve tracer.
2189 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
2190 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
2191
2192 checkpoint62y (2011/05/26)
2193 o pkg/seaice:
2194 - seaice_growth.F : in EVOLUTION branch, always include
2195 a_QSWbyATM_cover in qnet (as it should be).
2196 - verification/global_ocean.cs32x15 : update results accordingly
2197 (output.seaice.txt output_adm.seaice.txt).
2198 o pkg/seaice + obcs:
2199 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
2200 equivalent of assuming no tracer gradient outside the OB region.
2201 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
2202 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
2203 after changes above);
2204 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
2205 only at OB location (instead of over a band of OLx width).
2206 o pkg/seaice:
2207 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
2208 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
2209 o pkg/obcs:
2210 - split header file "OBCS.h" into 4 separated files:
2211 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
2212 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
2213 (contain no conditional statement which depends on OBCS options).
2214 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
2215 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
2216 o ctrl, cost, grdchk & autodiff pkgs:
2217 - make options file more standard (like other {PKG}_OPTIONS.h file but
2218 with AD_CONFIG.h); clean-up some of the included header files.
2219 o pkg/obcs:
2220 - do not mask tracer when applying OB (tracer == 0 could generate problems)
2221 - apply tracer OB values to tracer field only at OB location (instead of
2222 over a band of OLx width)
2223 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
2224 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
2225 obcs_apply_tloc.F & obcs_apply_sloc.F
2226 o obcs in model/src:
2227 - call OBCS_APPLY_W only if NonHydrostatic.
2228 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
2229 - reset dEtaHdt and wVel to zero outside OB interior region ;
2230 - leave tracer unchanged outside OB interior region: This has no effect
2231 on the solution but just to prevent unrealistic tracer value outside OB.
2232 - zero out velocity outside OB interior region: This has no effect on
2233 the solution but just to prevent unrealistic velocity outside OB.
2234 o obcs and non-lin free-surf:
2235 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
2236 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
2237 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
2238 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
2239 update results of test-exp. exp4(nlfs).
2240 o exp4 (nlfs) test-exp:
2241 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
2242 with NonLin-FreeSurf); update output.nlfs.txt
2243 o obcs and 2d/3d solver norm:
2244 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
2245 and outside OB interior region (will allow to place OB further inside the
2246 domain). Depending on the domain, can affects cg2d-Norm (previous
2247 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
2248 and cg3d-Norm (previous Norm was computed before canceling OB terms),
2249 e.g. in tutorial_plume_on_slope.
2250 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
2251 o pkg rbcs:
2252 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
2253 - add capability to apply relaxation to horizontal velocity uVel & vVel.
2254 o pkg/grdchk: add gradient check for control variable xx_shifwflx
2255 o pkg/shelfice/shelfice_init_fixed.F
2256 fix CPP-flag combinations
2257 o pkg/seaice: Merge iceage code of Pierre Rampal
2258 * update/change/correct ice age calculations
2259 * add age updates for pathological cases
2260 Probably needs more testing...
2261
2262 checkpoint62x (2011/05/13)
2263 o pkg/mom_vecinv:
2264 high-order vorticity scheme: use interior masks (maskInW & S)
2265 to zero-out (outside OB) gradient of vorticity.
2266 o verification exp.:
2267 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
2268 hs94.128x64x5 and seaice_obcs ; update results.
2269 o pkg/obcs:
2270 fix bug in OBeta for YZ sections in obcs_exf_load.F
2271 o pkg/ctrl, pkg/shelfice, and optim:
2272 - add new control variable xx_shifwflx (fresh water flux underneath ice
2273 shelves). This is almost as tedious as obcs-ctrl, because the
2274 variables needs its own mask.
2275 - add a cost function term that penalizes the deviation of xx_shifwflx
2276 from the first guess (zero) in analogy to other control variables
2277 o pkg/shelfice:
2278 - start basic adjoint
2279 o pkg/ctrl:
2280 - remove extra 2D field "for good measure" when initializing in
2281 ctrl_set_globfld_[xy/xz/yz].F
2282 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
2283 - improve error messages in ctrl_set_unpack_*
2284 o OBC implementation in momentum:
2285 use interior masks (maskInC,W & S) in momentum S/R:
2286 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
2287 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
2288 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
2289 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
2290 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
2291 (and also with Leith/Smagorinsky harmonic-viscosity).
2292 Update output of experiment dome and exp4 (+nlfs).
2293 o exp4 test-exp:
2294 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
2295 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
2296 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
2297 time-varying OB at Western-side for wVel (NonHyd); update output.
2298 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
2299 and biharmonic-viscosity ; also use prescribed time varying OB.
2300 o pkg/obcs:
2301 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
2302 o model/src:
2303 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
2304 - initialise startTime & nIter0 with unlikely values: allows to set one
2305 from the other without ambiguity.
2306 o seaice_obcs test-exp.:
2307 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
2308 o pkg/obcs:
2309 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
2310 no longer needed with maskInC,W,S in pkg/generic_advdiff.
2311 o pkg/seaice:
2312 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
2313 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
2314 - fixed bug in the initialization of sea ice salinity variable HSALT
2315 in seaice_init_varia.F (removed dependence on ICE2WATR)
2316 o fizhi-cs test exp.:
2317 switch reference output convention for these 2 non-standard test-exp,
2318 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
2319 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
2320 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
2321 o model/inc:
2322 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
2323 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
2324 o pkg/seaice:
2325 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
2326 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
2327 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
2328 and initial HSALT
2329
2330 checkpoint62w (2011/04/26)
2331 o pkg/mom_fluxform:
2332 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
2333 - use parameter "sideDragFactor" in no-slip BC side-drag part.
2334 - update output of exp. global_ocean.90x40x15
2335 o pkg/mom_vecinv:
2336 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
2337 o update seaice exp.:
2338 use more consistent parameter values (remove "backward compatability only":
2339 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
2340 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
2341 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
2342 o update test-exp global_ocean.90x40x15:
2343 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
2344 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
2345 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
2346 o turn on zStar & viscA4 in standard set-up (dir input/)
2347 and update output files: output.txt & output.dwnslp.txt
2348 o new AD-test experiment: obcs_ctrl
2349 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
2350 o pkg/dic:
2351 fix two bugs in handling water vapour pressure in carbonate chemistry
2352 and air-sea fluxes. Found by Val Bennington and Galen McKinley
2353 (add DIC Option = WATERVAP_BUG to recover old results)
2354 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
2355 o adding allowInteriorFreezing option to check for water below freezing point
2356 at depth and bring the negative heat anomaly to the surface level
2357 o pkgs _fields_load:
2358 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
2359 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
2360 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
2361 rbcs to get interpolation weights and time reccord number.
2362 - fix multi-threading in aim_fields_load.F
2363 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
2364 o external_fields_load:
2365 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
2366 interpolation weights) to use in a periodic time-series ; do not divide by
2367 time-step to convert to integer:
2368 - this fixes case where externForcingPeriod is not multiple of time-step
2369 (Thanks to Christopher L. Wolfe)
2370 - this fixes case where externForcingPeriod is an odd multiple of time-step
2371 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
2372 store index of time-record which is currently loaded:
2373 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
2374 - needed for the adjoint but not yet used because of extensive recomputations;
2375 (to be fixed soon)
2376
2377 checkpoint62v (2011/04/02)
2378 o verification/1D_ocean_ice_column added to test Ian Fenty's
2379 pkg/seaice_growth.F modifications for improving sea ice code differentiability
2380 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
2381 (new velocity statistics after changing maskInW & maskInS definition)
2382 o pkg/generic_advdiff with OBCS:
2383 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
2384 equivalent to assumption of no tracer gradient outside the OB region.
2385 This will affect the results if using obcs+biharmonic diffusion.
2386 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
2387 o pkg/obcs:
2388 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
2389 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
2390 in Interior region. No impact on solution but affects Velocity monitor stats.
2391 o pkg/ptracers (adjoint)
2392 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
2393 tape file for each tracer
2394 o model/inc/src and pkg/autodiff: add parameters that allow to turn
2395 of parts of the adjoint code at run time. For now, there are only
2396 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
2397 parameters are set in data.pkg.
2398 This is the lazy coward's version of doing this, but still useful for
2399 debugging. In order to do it right, everything needs to be moved to
2400 pkg/autodiff.
2401 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
2402 the end; this fixes the adjoint balancing code for open boundaries.
2403 o pkg/ctrl:
2404 - change behavior of xx_${varname}period to be analogous to exf-conventions:
2405 xx_${varname}period = 0., means time-independent control part
2406 xx_${varname}period = -12., means one-year-periodic monthly control part
2407 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
2408 clean up ctrl_init a little, remove unused variables
2409 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
2410 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
2411
2412 checkpoint62u (2011/03/15)
2413 o model/src:
2414 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
2415 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
2416 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
2417 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
2418 o pkg/ctrl/obcs/ecco:
2419 - remove obsolete, unused, and partially broken code:
2420 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
2421 ALLOW_CTRL_OBCS_BALANCE
2422 - put a stop statement into ecco/cost_obcsvol.F, but also add
2423 cost_obcsvol to ecco_ad_diff.list
2424 o pkg/ecco: fix counting cost function contributions for obcs (code
2425 by Matt M.) and diffkr for diagnostics
2426 o pkg/ecco, pkg/ctrl, pkg/grdchk:
2427 add cost penalty terms for initial uvel, vvel, eta controls
2428 and I/O for prior error files
2429 o pkg/mdsio:
2430 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
2431 (new argument) to check for tiled file in mdsioLocalDir : this fix the
2432 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
2433 o pkg/ctrl:
2434 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
2435 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
2436 unused and superfluous variables
2437 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
2438 o pkg/ecco
2439 - enable adjoint of Stevens OB
2440 o pkg/ctrl/ecco/grdchk:
2441 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
2442 Fortunately, we do not have any tests for the numerous cpp-flagged
2443 option of "obcs as control parameters" so we will never know
2444 if this is an improvement (but at least now things compile).
2445 - remove an obsolete initialization from ecco_cost_init_barfiles.F
2446 - fix some problems within never used ifdefs to make the code compile
2447 o pkg/obcs:
2448 - Refine Interior mask definition to work with more complex OB (e.g.
2449 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
2450 read in Interior mask from file. Check if Interior mask is consistent
2451 with OB list of indices.
2452 o pkg/seaice
2453 - beginning code for a seaice tracer package,
2454 but currently only used for seaice age: SEAICE_AGE
2455 SEAICE_num = 4
2456 iTracer = 1: area-weighted ice age
2457 = 2: volume-weighted ice age
2458 = 3, 4: template for one-year vs. multi-year ice
2459 data.seaice has new namelist SEAICE_PARM03 for arrays related to
2460 SEAICE_num
2461
2462 checkpoint62t (2011/03/05)
2463 o pkg/obcs:
2464 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
2465 then normal component. This ensures that the normal component is set
2466 correctly even when it conficts with tangential setting from an other OB.
2467 Affects results of test-experiment seaice_obcs: update the output.txt
2468 o pkg/obcs:
2469 - add code to monitor statistics of dynamical fields at OB.
2470 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
2471 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
2472 - change default: balance the Net inflow through all OB (instead of balancing
2473 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
2474 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
2475 to match Nortern OB inflow (OBCS_balanceFacN=0).
2476 o pkg/seaice:
2477 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2478 o pkg/seaice (seaice_growth v 1.113):
2479 - reverting seaice_growth to v 1.111 in order to have code with exact bit
2480 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
2481 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
2482 runtime flag SEAICEareaFormula is kept but is inactive
2483 o model/src:
2484 - add new param to scale curvilinear grid distance and area when using
2485 a different sphere radius from the grid-files.
2486 - test/check multi-threads EXCH applied to local variable (cg2d_x)
2487 o adjoint:
2488 - enable adjoint of Stevens OB
2489 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
2490 (a bit delicate because of potentially modified adj. common block structure;
2491 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
2492
2493 checkpoint62s (2011/02/15)
2494 o pkg/seaice (seaice_growth v 1.112):
2495 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
2496 computing the ice cover tendency from effective thickness tendencies. Include
2497 Ian Fenty's formula.
2498 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
2499 SEAICEareaFormula.
2500 - simplify notations for the various d_HEFF/d_AREA terms.
2501 o pkg/gmredi:
2502 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
2503 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
2504 add a verification test-run (front_relax.bvp) to test GM_useBVP.
2505 o pkg/seaice (seaice_growth v 1.111):
2506 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
2507 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
2508 also melt ice.
2509 o pkg/seaice:
2510 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
2511 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
2512 o pkg/cheapaml:
2513 - from Nico Wienders: New version of this package.
2514 o pkg/flt:
2515 - add CPP options to prevent floats to re-enter the opposite side of
2516 a periodic domain (default: keep periodicity)
2517 o pkg/gmredi:
2518 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
2519 (needed for multi-dim advection).
2520 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
2521 o model/src:
2522 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
2523 o tutorial_tracer_adjsens
2524 - extend to NLFS and replace maskC by hFacC
2525 (change reference output accordingly)
2526
2527 checkpoint62r (2011/01/24)
2528 o testreport:
2529 - add option -deloutp (-do) to remove output file after successful run
2530 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
2531 extract exact list of procs from this file ; adjust COMMAND by
2532 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
2533 o pkg/ecco: replace old ineffective way of penalizing deviations from
2534 first guess (of obcs) with code by Matt Mazloff
2535 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
2536 exf/cal
2537 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
2538 and handle case of obcs?period == 0
2539 Not affected by these changes: There is still an inconsistency in
2540 the computation of start/endrec for the obcs variables for ALLOW_CAL
2541 defined (see comment by Menemenlis, 7-Mar-2003)
2542 - make S/R ctrl_get_gen_rec return something meaningful even if
2543 ALLOW_CAL is not defined
2544 - ctrl_getobcs?: simplify code so that it does not need to use
2545 S/R exf_swapfields
2546 o testreport:
2547 allow to test MPI with different number of processors for each experiment:
2548 create file "SIZE.h.mpi" in each build dir.
2549 Note: update of "-command" argument not yet implemented.
2550 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
2551 alleviate the need for additional 3D tapes when using
2552 the non-inear free surface in the adjoint. This is done
2553 by adding an 'update' of hfacc etc. to their current
2554 value at the beginning of forward_step.F.
2555 o pkg/seaice
2556 seaice_lsr: move stress-divergence computations out of outer pseudo-
2557 timestepping loop
2558 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
2559 up, so that the calls of the ctrl_* subroutines are really at the end
2560 of the routine.
2561 o pkg/gmredi:
2562 allow to specify a 2-D horizontal map and a 1-D vertical profil
2563 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
2564 o pkg/seaice:
2565 move lsr iterations from seaice_dynsolver to seaice_lsr.
2566 o pkg/seaice:
2567 reduce memory footprint of seaice mutldim advection tapes,
2568 by using a 2D tape independent of the generic_advdiff ones,
2569 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
2570
2571 checkpoint62q (2010/12/29)
2572 o model/src:
2573 - check horizontal grid-spacing for unset or zero/negative values.
2574 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
2575 o pkg/flt:
2576 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
2577 - precision of input and output files set according to readBinaryPrec
2578 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
2579 - initial float position from tiled file was not converted to index space
2580 (looks like a bug): fixed to make it similar to initial pos. global file.
2581 o global_ocean.cs32x15:
2582 change SIZE.h of AD set-up to get same tiling as with MPI.
2583 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
2584 o model/src:
2585 add flag to control printing of domain fields (bathymetry, hFac ...) in
2586 ini_mask_etc (call to plot_fieds_xy*).
2587 o pkg/thsice:
2588 if useEXF, some forcing fields are not valid in overlap: fixed by computing
2589 over the interior only + apply EXCH at the end (like with SEAICE advection).
2590 o pkg/mdsio:
2591 - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
2592 to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
2593 - change barrier call for safe multi-threads access to 3-D shared buffer.
2594 - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
2595 - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
2596 remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
2597 o pkg/flt:
2598 - add fourth-order Runge-Kutta integration
2599 - add basic exch2 support (only 1 facet supported so far!)
2600 o pkg/mdsio+rw:
2601 new S/R to read local (or tile independent) vector (read counterpart of
2602 mds_writevec_loc, and front-end write_glvec_rl/rs).
2603 o global_ocean.cs32x15: additional input_ad.seaice experiment
2604 that uses pkg/seaice rather than pkg/thsice.
2605 (using multidim advection for seaice)
2606 o towards more F95 syntax for array specification in namelist:
2607 - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
2608 of all verification experiments.
2609 e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
2610 was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
2611 - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
2612 o global_ocean.cs32x15: additional input.seaice experiment
2613 that uses pkg/seaice rather than pkg/thsice.
2614
2615 checkpoint62p (2010/12/17)
2616 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
2617 to THSICE_SIZE.h to avoid conflict with pkg/seaice.
2618 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
2619 allow for use of multim. advection in seaice adjoint.
2620 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
2621 - first attempt to close budgets by taking into account the freshwater
2622 flux implied by the sublimation of snow and ice. So far only the
2623 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
2624 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
2625 o eesupp/src:
2626 new S/R with new option (NML_EXTENDED_F77) to change array specification
2627 from F95 standard to commonly accepted extended F77 form.
2628 This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
2629 and to revert back to the original syntax (with -DNML_EXTENDED_F77)
2630 for less tolerant f77 compiler (e.g., pgf77, g77).
2631 o globalFiles:
2632 commented out in parameter file "data" since it's not safe with MPI
2633 (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
2634 in this case); no longer commented out in restart test (tst_2+2).
2635 o add adTapeDir to specify a special directory where adjoint tapes are
2636 written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
2637 and cannot be used together with mdsioLocalDir.
2638 o nesting pkgs:
2639 - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
2640 - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2641 - add parameter files + utils dir + output from short run on beagle.
2642 o pkg/seaice:
2643 fix seaice_growth.F store directives; update results of exp. lab_sea.ad
2644 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
2645 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
2646
2647 checkpoint62o (2010/11/25)
2648 o pkg/exf:
2649 - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
2650 o pkg/seaice:
2651 - seaice_ocean_stress: split a loop for better vectorization of the
2652 adjoint code
2653 - seaice_growth.F: fix bug in conservation of freshwater connected to
2654 capping of heff, put contribution into d_HEFFbyNEG
2655 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
2656 by something more sensible (parameters that are what their name implies)
2657 - change some defaults, so that by default exf-parameters are used for
2658 things like rhoAir, cpAir,latent/sensible heat parameters, in order
2659 to reproduce the old results, many data.seaice now contain funny values
2660 for cpAir and latent heat of sublimation
2661 o packages_readparms.F: move exf_readparms up in line so that
2662 exf-parameters are visible for other packages (e.g. seaice)
2663 o debugMode & debugLevel=2:
2664 - differentiate between debugMode & debugLevel=2:
2665 debugMode: controls printing of debug messages (sequence of S/R calls).
2666 debugLevel: controls printing of algorithm intermediate results and stats.
2667 - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
2668 => allows to print debug-stats without all sequence of call messages.
2669 - switch control of debug print from debugLevel to debugMode in many S/R.
2670 o pkg/obcs (obcs-sponge):
2671 fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
2672 call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
2673 o pkg/generic_advdiff:
2674 - record overlap minimum size for each advection scheme;
2675 - refine criteria on overlap minimum size;
2676 - check and stop (in gad_check) if overlap size is too small.
2677 o pkg/obcs:
2678 - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
2679 once, in ptracers_implicit.F)
2680 - with seaice: remove test on empty file name in obcs_apply_seaice (always
2681 apply OB values when tile has OB)
2682 o model/src, coriolis setting:
2683 - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
2684 useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
2685 files (selectCoriMap=3) with any grid.
2686 - add parameter "fPrime" for constant second Coriolis coeff (default=0).
2687 o pkg/seaice/seaice_growth.F:
2688 a few cosmetic changes that reduce the number of lines of code
2689 o pkg/obcs: add boundary conditions following Stevens (1990)
2690 - the code follows old MOM/NAOSIM code
2691 - so far it is only implemented for the eastern and western boundaries
2692 and NOT for pTracers
2693 o pkg/rbcs:
2694 - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
2695 beginning of the first rbcs forcing period.
2696 - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
2697 offline package, i.e., one file per time, labeled by iteration number;
2698 deltaTrbcs sets the timestep with which the data was generated;
2699 rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
2700 - rbcsForcingCycle=0 makes forcing non-cyclic.
2701 - make arithmetic safe for negative times and odd forcing periods.
2702
2703 checkpoint62n (2010/11/09)
2704 o pkg/seaice:
2705 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
2706 o pkg/obcs:
2707 New S/R to copy tracer value from the OB location to narrow band region
2708 (width = same as overlap) beyond the OB: preserve OB value (needed for
2709 high-order scheme) which were overwritten by EXCH call if in overlap
2710 region. Applied to theta, salt, ptracer and advected seaice variables.
2711 With seaice: use maskInC in similar way as in gad_advection.F,
2712 in seaice_advection.F and advect.F.
2713 Update output of experiment seaice_obcs and change exp4 to test OBCS with
2714 4th order Adv.Scheme. for pasive salt and ptracer.
2715 o tools/genmake2:
2716 - when looking for an optfile (not specified), only search for Fortran compiler
2717 (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
2718 - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
2719 (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
2720 - set default for CPP to "cpp -traditional -P" (was the case without specifying
2721 an optfile, but otherwise default was just "cpp".
2722 - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
2723 - when "CC" is not set in the optfile, look for possible C compiler
2724 (instead of just setting CC=cc)
2725 - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
2726 => add a ".F" to ".o" rule for source files with no "#include" (such as
2727 port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
2728 - move gfortran before g77 in list of possible Fortran compiler (consistent
2729 with reference compiler switch from g77 to gfortran)
2730 o pkg/seaice:
2731 o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
2732 seaice_check that stops the model, when the CPP flag is used.
2733 o seaice_growth.F: make capping of ice volume conserving by returning the
2734 capped ice as freshwater to EmPmR. This does not change the verification
2735 experiments but will change runs where the capping is acutally active
2736 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
2737 (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
2738 global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
2739 lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
2740 o tools/genmake2:
2741 - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
2742 - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
2743 - clean previous genmake log files before anything else.
2744 - change Makefile to remove testreport log files (*.tr_log) and genmake log
2745 files only with "CLEAN" target (instead of "Clean");
2746 o pkg/generic_advdiff:
2747 Change OBCS in multiDim advection (gad_advection.F):
2748 Use maskInC to prevent intermediate update of tracer-field in OB regions,
2749 thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
2750 which were applying future time-step OB values.
2751 This way, all explicit calculations use current-time-step OB values
2752 (simpler and more consistent).
2753 Affects results when set-up uses time-varying OBC and multi-dim advection;
2754 update output of experiment seaice_obcs.
2755 o pkg/seaice:
2756 move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
2757 this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
2758 SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
2759 Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
2760 but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
2761 unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
2762 o pkg aim (2010/10/26):
2763 - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
2764 formulation with obliquity, eccentricity, ... as run-time parameters,
2765 - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
2766 upward shortwave radition at the surface (all-sky and clear-sky).
2767 o pkg/obcs:
2768 - writing sections with globalFiles=T does not work: switch to tiled-files
2769 when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
2770 - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
2771 - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
2772
2773 checkpoint62m (2010/10/21)
2774 o pkg/seaice: vectorize seaice_solve4temp.F
2775 - move iterations loops outside of i/j-loops
2776 - requires 2D arrays for TB and effConduct
2777 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
2778 modified in this routine
2779 - a little bit of clean up, adjusting indentation, etc.
2780 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
2781 performance and '**TWO' by '**2' (because TWO is a float),
2782 replaced ONE, ZERO
2783 o eesupp/src:
2784 fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
2785 o pkg/seaice/seaice_growth.F
2786 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
2787 merging process. The merged routine has two branches, and one activates the 'evolution'
2788 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
2789 In summary, here is what the '10/10 revision' did consist of
2790 part 1: seaice_growth.F revisions 1.71 to 1.75
2791 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
2792 The emphasis here was on improving readability (e.g. by trying to use meaningful
2793 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
2794 part 1.5:
2795 - revising the lab_sea experiment to make it a more useful (i.e. stable
2796 and representative of an actual model run). This was done by generating a
2797 (winter) pickup to start from, switching back the main experiment dynamic
2798 solver from evp to lsr, having one of the experiments use the free drift solution.
2799 part 2: seaice_growth.F revisions 1.76 to 1.85
2800 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
2801 - Sorting out the various fields units and sign (set early on and reset at the end)
2802 to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
2803 fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
2804 - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
2805 and simplifying logical expressions to further improve readibility.
2806 part 3: seaice_growth.F revisions 1.86 to 1.89
2807 - Re-organize the blocks of code more logically.
2808 - Merging the '_if.F' pieces that add something new.
2809 o pkg/thsice:
2810 - vectorize thsice_solve4temp and thsice_get_exf.
2811 Problem: thsice_solve4temp has an unvectorizable statement that
2812 might also be problematic for TAF
2813 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
2814 does not change the verifcation experiment, but will change all
2815 experiments that have this flag undefined (not tested in verification);
2816 a little reorganization to save a few 2D fields and recomputations
2817 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
2818 - 2nd step: fix some store dirs
2819 o seems to work somewhat, i.e. using ifort but not g77
2820 o likely cause are incomplete init. or recomputation
2821 o start verification/global_ocean.cs32x15/input_ad.thsice
2822 o pkg/obcs: add support for exch2
2823 - the position of the boundary and prescribed values are specified using
2824 a global domain with exch2 facets stacked
2825 - in x for N,S boundaries (like W2_mapIO=-1)
2826 - in y for E,W boundaries (so E,W boundaries do not overlap)
2827 o pkg/mdsio: add support for writing global sections with exch2
2828 file layout is as for obcs described above:
2829 - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
2830 - for y-z sections, facets are stacked in y
2831 o pkg/thsice:
2832 - change a few routines for better vectorization: thsice_albedo.F,
2833 thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
2834 not affected, but in particular the latter routine has changed
2835 dramatically (not necessarily easier to read now).
2836 - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
2837 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
2838 o verification/lab_sea:
2839 - overhaul of the forward model experiments. The main motivation
2840 for this revision is that lab_sea has proven quite fragile (when
2841 changing the sea-ice code, and switching platforms) to a point
2842 when failures were very hard to attribute to specific code problems.
2843 - the suspected reason for this fragility is noise amplification by evp so,
2844 to start with, we decided to replace evp with lsr in the main experiment.
2845 - the input.lsr experiment thus became obsolete and was removed.
2846 - it was replaced with the input.fd experiment that uses an
2847 analytical "free drift" solution as the ice velocity field.
2848 - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
2849 will hopefully allow us to discriminate problems due to dynamic solvers
2850 from problems due to the thermodynamic code. input.salt_plume (lsr) allows
2851 us to test additional options, along with the salt plume package.
2852 - Finally a pickup was generated (at the end of a one year run) to
2853 make the tests more representative of an actual model run. Previously
2854 the tests starting point was a 1m thickness of ice everywhere.
2855 o pkg/seaice:
2856 - introducing S\R seaice_freedrift.F that compute the
2857 analytical solution to an approximate ice momentum
2858 equation (i.e. the simple stress/coriolis balance).
2859 - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2860 of the free drift velocity field, and enable its use.
2861 To actually use the free drift solution as the model ice
2862 velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
2863 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
2864
2865 checkpoint62l (2010/10/04)
2866 o pkg/seaice:
2867 -fix the USE_ORIGINAL_SBI version (for variable freezing point);
2868 -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
2869 version (with USE_ORIGINAL_SBI undef);
2870 o add hooks for new packages OASIS, the package will follow
2871 (hooks exclude the seaice pkg for now)
2872 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
2873 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
2874 rather than mdsio_readvector.F/mdsio_writevector.F, within
2875 adread_adwrite.F to read/write adjoint-related tapes to disk.
2876 o eesupp and pkg/mdsio: ALLOW_WHIO
2877 Option to write/read 2D fields to files including tiles halos.
2878 The main purpose is for adjoint related "tape I/O".
2879 The secondary purpose is for debugging phases.
2880 A word on those rather specifically intended purposes.
2881 The code was meant to be stripped down to the bare minimum.
2882 Typically, there is a unique and basic mapping to the global
2883 buffer (tile by tile, then proc by proc, then level by level), and
2884 byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
2885 meant to generate user friendly outputs of various shapes and forms.
2886 Rather it is intended, for the knowledgeabale developers,
2887 to be largely independent of the many mdsio options, to allow
2888 outputs of tiles+halos in debugging phases and in adjoint runs,
2889 and to allow some flexibility in tuning (adoint) I/O depending on each
2890 file system behavior. With regard to tuning, most of the potential knobs
2891 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
2892 to specify directories, to specify the typical size of I/O calls, etc.)
2893 are not yet included, and will be added if they prove useful.
2894 o pkg/seaice:
2895 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
2896 o pkg/seaice:
2897 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
2898 code (seaice_budget_ice_if.F) which enable to recover old standard
2899 code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
2900 temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
2901 o model/src (rStar):
2902 use simple average (not area weighted) of rStarFac at U,V point when using
2903 vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
2904 update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
2905
2906 checkpoint62k (2010/09/17)
2907 o adjoint
2908 * changed verification/global_ocean.cs32x15 ; adjoint now tests
2909 Adams-Bashforth 3 + NLFS + RSTAR
2910 * some more modifs required for ECCO-GODAE v4
2911 o pkg/seaice
2912 add SEAICE_AGE_VOL option to use volume instead of area for
2913 integrating SEAICE_AGE
2914 o model/src:
2915 first check-in of sigma & hybrid-sigma coordinate code ; also includes
2916 non-linear free-surface parts ; but pressure-gradient not yet coded.
2917 o pkg/ptracers:
2918 option for ptracer to convert Salt Relax into additional EmP.
2919 tested in exp. global_ocean.90x40x15.dwnslp (update output)
2920
2921 checkpoint62j (2010/08/25)
2922 o pkg/ggl90:
2923 other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
2924 o pkg/dic: car_flux.F, phos_flux.F
2925 - reduce number of exp-calls in order to improve performance
2926 - clean up a little (replace fields by their macros, etc., fix
2927 typo in CPP-flag)
2928 o pkg/ggl90: minor changes
2929 - GGL90diffKrS was removed --> always use GGL90diffKr
2930 - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
2931 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
2932 (commented out for now)
2933 - change in max/min operations to ensure that smoothing is ok
2934 - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
2935 - always use diffKrNrT as background profile (i.e. never use diffKr field)
2936 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
2937 o pkg/dic:
2938 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
2939 vectorization
2940 - small bug fix in insol for the unlikely case of a cartesian grid
2941 - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
2942 + now vectorize, which also removes adjoint recomputations;
2943 + replace integer maksp1 by _RL maskp1
2944 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
2945
2946 checkpoint62i (2010/07/21)
2947 o pkg/flt:
2948 - with OBCS: stop floats which enter the OB region
2949 o model/src:
2950 - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
2951 for implicit vertical advection.
2952 o pkg/seaice:
2953 - account for melting in seaice age evolution.
2954 - remove double counting of seaice ridging effect on seaice age.
2955
2956 checkpoint62h (2010/06/18)
2957 o pkg/exch2:
2958 - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
2959 o tools/genmake2
2960 - remove "-pdefault" option: redundant with the use of "packages.conf";
2961 - remove file pkg/pkg_default : set the default as a pkg group
2962 ("default_pkg_list") defined in pkg/pkg_groups;
2963 - fix for case pkg/pkg_depend is missing (was hanging before);
2964 - add option "-pgroups" to specify a different pkg_groups than the default.
2965 o verification/adjustment.cs-32x32x1:
2966 add a "minimal" set-up test (code_min & input_min) which only compiles
2967 eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
2968 o tools/genmake2
2969 - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
2970 - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
2971 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
2972 files are nearly the same anyway.
2973 Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
2974 - redefinition of tau(i,i) (by a factor of ustar)
2975 - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
2976 - replace rhonil by rhoConstFresh in computation of evap (bug fix)
2977 - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
2978 - replace
2979 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
2980 shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
2981 by
2982 shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
2983 (changes results)
2984 -> exf_bulkformulae v1.22,
2985 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
2986 (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
2987 output.txt 1.63
2988 offline_exf_seaice: output.seaicetd.txt 1.7
2989 seaice_obcs: output.txt 1.10)
2990 Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
2991 -> exf_bulkformulae v1.23,
2992 unfortunately requires updating lab_sea.salt_plume (6 matching digits),
2993 and global_ocean.cs32x15.icedyn (only 11 matching digits)
2994 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
2995 o adjoint of exch-1:
2996 - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
2997 (note: was already like this when using EXCH-2) and remove flow dir
2998 and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
2999 - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
3000 - update pkg/exch2 diff list.
3001
3002 checkpoint62g (2010/05/19)
3003 o eesupp/src (exch-1):
3004 - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
3005 and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
3006 (renamed to exch1_*rx_cube.F).
3007 - change accordingly exch_*_rx.template and AD version in pkg/autodiff
3008 to call new exch1 S/R ; update Makefile and .cvsignore.
3009 - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
3010 exch2_xy_rx later)
3011 Note: after updating your code, need to run "make clean" in eesupp/src
3012 o test experiment bottom_ctrl_5x5:
3013 new output_adm.txt with fewer grdchk & less monitor output.
3014 o model/src:
3015 remove the call to ini_cori in initialise_varia.F (just keep the usual one
3016 in initialise_fixed.F). More consistent with coriolis & horizontal grid
3017 beeing treated in the same way (ini_grid is not called a 2nd time).
3018 o pkg/exf:
3019 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
3020 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
3021 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
3022 - cosmetic changes to exf_bulkformulae.F to make it look more like
3023 exf_bulk_largeyeager04.F
3024 o eesupp/src (exch-1):
3025 - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
3026 - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
3027 array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
3028 (even without using MPI).
3029 - Message mode: move RecvAck setting (indicator of buffer being ready)
3030 from send_put to recv_get S/R (was useless before, but not sure if
3031 it's much more useful now);
3032 - Switch the order of sync: MPI-proc 1rst and then threads;
3033 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
3034 - fix AD code for communication mode ='get' (but not used).
3035 o model/src:
3036 initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
3037 not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
3038 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
3039 o pkg/ctrl: require a specific set of control variables and exf-flags for
3040 adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
3041 o model/src:
3042 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
3043 1rst forward sweep, to avoid over-writing output files during recomputations
3044 recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
3045 b) 2nd version:
3046 - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
3047 - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
3048 writePickupAtEnd) + seaice & ptracers output;
3049 - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
3050 o model/src:
3051 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
3052 o pkg/exch2:
3053 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
3054 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
3055 o pkg/autodiff & exch2:
3056 process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
3057 (for now, only if ALLOW_EXCH2 is defined).
3058 o pkg/autodiff:
3059 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
3060 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
3061 + clean-up comments (_RS is not always real*4)
3062 - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
3063 - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
3064 was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
3065 o testreport (AD-tests):
3066 no longer link files from dir "../input" (1rst link files from
3067 "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
3068
3069 checkpoint62f (2010/04/29)
3070 o model/src/the_main_loop.F:
3071 adjust store directives for seaice evp and multicategory according to
3072 pkg/ecco/the_main_loop.F
3073 o adjoint:
3074 global_sum_ad was incomplete (noted many times by many people ;)
3075 nice description by Jean U. as follows:
3076 * allreduce(var) in global_sum.F can be interpreted as
3077 reduce(sum) followed by broadcast of sum.
3078 * The adjoint of that is
3079 sum(adjoint) followed by broadcast(summed adjoint value)
3080 or in other words, allreduce(sum, adjoint vars)
3081 We were missing the sum(adjoint)!
3082 Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
3083 (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
3084 The fix should produce 16-digit accuracy between
3085 single-CPU multi-tile (e.g. nSx=2, nPx=1) and
3086 multi-CPU single-tile (e.g. nSx=1, nPx-2)
3087 We'll probably change this yet again shortly
3088 o eesupp/src:
3089 - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
3090 o pkg/icefront
3091 - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
3092 specification of addmass array based on a 2D field, which is added
3093 at bottommost wet level at each horizontal location.
3094 o model/src:
3095 horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
3096 layout; (not always compatible with delX,delY setting; commented out for now).
3097 o pkg/exch2:
3098 change tile to processor setting (case nSy*nPy > 1): allows default model mapping
3099 (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
3100
3101 checkpoint62e (2010/04/15)
3102 o pkg/obcs:
3103 - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
3104 o pkg/dic:
3105 -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
3106 (note: not presently tested in any forward verification exp.)
3107 update tutorial_global_oce_biogeo AD output file.
3108 o pkg/exf:
3109 - account for the variation of albedo as a function of zenith angle
3110 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
3111 o build_options:
3112 - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
3113 o pkg/dic:
3114 change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
3115 - use binary pickup file for restart;
3116 - initialise atmos-CO2 box from dic_pCO2 parameter;
3117 - fix multi-threaded.
3118 o pkg/rbcs:
3119 - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
3120 change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
3121 - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
3122 and update output.txt
3123 o pkg/kpp:
3124 - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
3125 - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
3126 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
3127 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
3128 - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
3129 KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
3130 o pkg/offline:
3131 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
3132 (bug was added in version 1.10 on 2007-08-23).
3133 o pkg/offline:
3134 - no need to specify periodicExternalForcing, etc ... to use offline pack
3135 - offline input files no longer just single prec --> parameter offlineLoadPrec
3136 o verification/lab_sea:
3137 change AD test to multi-tile setup and update all 4 AD output.
3138 NOTE: while cost function values remain very similar,
3139 gradients are very different, although gradient checks are self-consistent
3140 Should try to get to the bottom of this (cost function summation order?)
3141 o pkg/dic:
3142 in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
3143 a weakness of TAF that drops part of double precision in log10 derivative.
3144 <= changes removed since problem has been fixed in current TAF version 1.9.71
3145 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
3146 o pkg/ecco:
3147 add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
3148 update all 4 lab_sea AD output.
3149
3150 checkpoint62d (2010/03/22)
3151 o build_options:
3152 remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
3153 o remove unbalanced quote (single or double) in commented line of source code
3154 (may cause some warning with some preprocessor/makedepend versions).
3155 o pkg/seaice:
3156 fix seaice_model.F for adjoint (gael) and update AD results of experiments
3157 lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
3158 o testreport:
3159 add option '-runonly' (short: '-ro') to just do the run part (without make).
3160 o eesupp: remove JAM communication code (obsolete).
3161 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
3162 (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
3163 to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
3164 (update also the output).
3165
3166 checkpoint62c (2010/03/02)
3167 o tools/build_options :
3168 move (some) old optfiles from build_options/ to build_options/unsupported/
3169 o model/src and pkg/exf
3170 surface relaxation -- separating data and data.exf options
3171 The point is to ensure that we specify the surface relaxation
3172 either in data or in data.exf (but not half and half) and to
3173 avoid an accidental relaxation to 0 (which happened if a time
3174 scale was specified but the file name was left empty)
3175 o model/src model/inc and pkg/mom_common
3176 ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
3177 => addition to the viscosity field as computed by others schemes
3178 o tools/build_options:
3179 - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
3180 but keep the former optfile for few weeks for smooth transition
3181 o pkg/ecco
3182 - allow user defined cost function contributions
3183 CPP: ALLOW_USERCOST_CONTRIBUTION
3184 USAGE: compute contributions in cost_usercost_all.F
3185 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
3186 the two options are complementary.
3187 o pkg/smooth
3188 - migration from contrib to the main repository
3189
3190 checkpoint62b (2010/01/26)
3191 o pkg/monitor:
3192 - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
3193 (in case someone forgot to update customized pieces of code)
3194 o nonHydrostatic:
3195 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
3196 - add a simple 2-D experiment (short_surf_wave) to test it.
3197 o pkg/icefront:
3198 adding the shell of, and the hooks to, a new package that
3199 will model melting and freezing of vertical glacier ice fronts
3200 o momentum:
3201 add diagnostics of momentum tendency from Hydrostatic pressure gradient
3202 (without surf.pressure term: would need a 2nd filling since implicit term).
3203 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
3204 two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
3205 cannot deal with the former
3206 o cleaning:
3207 - remove all (except OpenAD) old TLM output from results_ad dirs.
3208 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
3209 - comment out maskH definition (replaced by maskInC)
3210 o pkg/monitor:
3211 - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
3212 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
3213
3214 checkpoint62a (2010/01/15)
3215 o model/src:
3216 - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
3217 o pkg/diagnostics:
3218 - add optional level number diagnostics (i.e., level number to be define
3219 explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
3220 - strictly check for valid parser-code(10) ;
3221 - check if adding diag to the list from the right place.
3222 o pkg/longstep:
3223 - change parameters and fix tracer conservation with rstar/nonlinear free surface
3224 o diagnostics:
3225 - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
3226 S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
3227 o pkg/diagnostics:
3228 - Add option for writing vertical integral (sum of selected levels) of an output
3229 field instead of writing output field levels. Activate this option on a per
3230 output-file basis, by setting the 2nd character of fileflag to 'I'.
3231 - Add field-specific information relative to level integral in 3rd postion
3232 of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
3233 vertically (x level-thickness x hFac), "r"=same but without hFac.
3234 o do_the_model_io:
3235 - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
3236 in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
3237 writing pickups and stopping.
3238 o pkg/diagnostics (for now, only with mdsio):
3239 - write time information to meta file (and modify accordingly rdmds.m) :
3240 time-averaged diagnostics output: write starting and ending time of the
3241 time-averaging interval ; snap-shot diagnostics output remains unchanged;
3242 o pkg/timeave:
3243 - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
3244 always Nr), now assumed to be equal to number of levels of averaged field;
3245 only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
3246 o pkg/sbo:
3247 - fix ocean bottom pressure global-average & 2-D time-ave output (was
3248 neither initialised nor filled).
3249 - add starting iteration in suffix of global-average output file
3250 (to avoid over-writing the file after a restart)
3251 - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
3252 o time-average:
3253 - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
3254 (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
3255 ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
3256 this fix DIC_COST cumulative-time array (previously: bi,bj,k)
3257 - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
3258 - fix missing accumulation for pkg/opps.
3259 - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
3260 (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
3261 - fix initialisation of time-ave vars and do only full time-step increment
3262 (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
3263 o pkg/layers:
3264 - use standard RW pkg S/R to write the output
3265 and remove local write_fld version (which had a problem).
3266 - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
3267 - fix LAYERS_CALC argument list.
3268 o pkg/timeave:
3269 - store cumulative-time in a simple tiled array (drop the level index)
3270 - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
3271 o pkg/ocn,aim_compon_interf
3272 - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
3273
3274 checkpoint62 (2009/12/23)
3275 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
3276 (was not previously tested in any other exp.)
3277 o pkg/monitor:
3278 - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
3279 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
3280 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
3281 - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
3282 - change del2 calculation.
3283 - use interior masks (instead of maskH, <- to be remove).
3284 - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
3285 o mask & obcs:
3286 - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
3287 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
3288 (called after packages_init_fixed)
3289 o pkg/obcs:
3290 - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
3291 Fixes bug in obcs+exf with nSx*nSy.GT.1
3292 - fix multi-tile handling in obcs balance code
3293 o nonHydrostatic:
3294 - Implement AB-3 for non-hydrostatic vertical momentum ;
3295 (change ordering of var. stored in pickup file when using NH)
3296 - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
3297 - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
3298 (in prep. for new NH free surface form).
3299 o pkg/obcs:
3300 add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
3301 o model/src:
3302 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
3303
3304 checkpoint61z (2009/12/01)
3305 o nonHydrostatic:
3306 Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
3307 a spurious source of energy in simple baroclinic adjusment test case.
3308 Update all non-hydrostatic exp output.
3309 o model/src (3-d solver):
3310 Change again 3-D solver free-surface RHS term when exactConserv=T:
3311 simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
3312 (which was not the case with previous formulation).
3313 To recover previous version, just reset "oldFreeSurfTerm" to previous value.
3314 Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
3315 o nonHydrostatic:
3316 - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
3317 for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
3318 - change 3-D solver to work with r* (for now, only with linear free-surf.)
3319 - add few debug diagnostics (cg3d_x, residual)
3320 o model/src:
3321 fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
3322 update output of exp. global_ocean.cs32x15.viscA4
3323 o update output of exp. global_ocean.cs32x15.icedyn after removing
3324 #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
3325 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3326 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
3327 for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
3328 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
3329 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
3330 runtime flag useSRCGSolver. Modify verification experiment global_with_exf
3331 to test this code
3332 o pkg/cd_code:
3333 Change defaut D-grid time-stepping to get the same for D-grid momentum as for
3334 C-grid momentum. D-grid velocity used to be stepped forward in time with
3335 Adams-Bashforth only on surface pressure term. Tests show that using AB on
3336 D-grid coriolis term improves stability (as expected from CD-scheme paper).
3337 To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
3338 Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
3339 lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
3340 tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
3341 Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
3342 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
3343 o pkg/obcs:
3344 - fix bug in initialisation (broken since Oct 1rst modification)
3345 for useOBCSprescribe without useEXF.
3346
3347 checkpoint61y (2009/11/15)
3348 o pkg/seaice
3349 - change (once again) the discretization for the evp solver: rather than
3350 squaring the averages of strain rates, average the squares to give
3351 a better approximation to VP behavior (in simple test); this breaks
3352 verification experiments that use EVP (lab_sea and lab_sea.hb87)
3353 --> update outputs
3354 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
3355 to improve vectorization of adjoint code on TARGET_NEC_SX
3356 o verification/vermix:
3357 - change vermix to a more "classical" 1d column with high vertical
3358 resolution, seasonal heat flux forcing and constant wind forcing
3359 --> update outputs
3360 o pkg/seaice
3361 - fix diagnostics of principal stress components for EVP
3362 - add optional diagnostics of non-linear convergence for LSOR solver
3363 - make maximum zeta a runtime parameter
3364 o model/src (3-d solver):
3365 Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
3366 which consisted in removing the Surf. Non-Hydrostatic pressure from the
3367 whole column and adding it to Eta (inspired from Casualli, 1999):
3368 Only affects 3-D solver initial guess and only if using ExactConserv,
3369 but tests did show a degradation of solver convergence. For this reason,
3370 decide to disable this piece of code.
3371 to recover previous version, just set zeroPsNH = exactConserv (line 78).
3372 Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
3373 o pkg/ggl90:
3374 - fix previous modif (unfortunatly has not been documented here).
3375 o pkg/seaice/autodiff:
3376 - add CPP flag to include clipping of zeta in EVP code;
3377 although clipping of zeta is not necessary for EVP and not recommended
3378 it was done by default, now clipping is disabled by default
3379 - modify computation and store zetaC/Z in seaice_evp for TAF
3380 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
3381 - change seaice_calc_viscosities/strainrates for better
3382 vectorization after AD by TAF
3383 - rearrange common blocks in SEAICE.h once again for easier dumps of
3384 adjoint output, adjust adcommon.h and g_common.h
3385 - change flux form of default advection scheme for better vectorization
3386 of adjoint code
3387 - modify lab_sea/input.lsr to test the flux form of default advection
3388 scheme
3389 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
3390 transition in checkpoint61r)
3391
3392 checkpoint61x (2009/10/19)
3393 o adjoint: adding two new verification experiments
3394 * tutorial_global_biogeo: an online dic sensitivity experiment
3395 (work with G. Forget)
3396 * tutorial_dic_adjoffline: an offline dic sensitivity experiment
3397 (an update of the Dutkiewicz et al., 2006 paper)
3398 Both use the same CO2FLUX cost function, but different controls
3399 Gradient checks look good, but some recomp. could still be traightened out
3400 Should add xx_dic control variable to test at some point
3401 o model/src:
3402 add run-time parameters to check and/or mask initial Temp & Salt
3403 o pkg/ptracers:
3404 apply zonal filter (if used) to all passive tracers
3405
3406 checkpoint61w (2009/10/12)
3407 o adjoint:
3408 * update and finish work on adjoint of dic package (G. Forget)
3409 * start adjoint of offline package
3410 * bug fix for cube-sphere TLM code (active_file_g.F)
3411 o tutorial_global_oce_optim:
3412 now tested with 4 tiles (change data.grdchk and update output_adm.txt)
3413 and add SIZE.h_mpi for MPI testing
3414 o pkg autodiff
3415 - fix bug in autodiff_restore
3416 - make genmake2 remove comments and empty lines from ad_input_code.f in
3417 order to reduce file size (new script file remove_comments_sed)
3418 o allows to specify vertical profile of vertical viscosity (viscArNr)
3419 o pkg autodiff
3420 autodiff_ini_model_io: comment out writing of grid information to netcdf
3421 files, because at this time the grid fields are a bunch of zeros
3422 (this is analogous to ini_mnc_vars.F)
3423 o pkg seaice/autodiff:
3424 left-over from removing the 3-time-level fields:
3425 - small rearrangement of common blocks (SEAICE.h)
3426 - fix field declaration in order to get meaningful output in
3427 adseaice.*.nc (adcommon.h)
3428 o pkg obcs:
3429 - go through NH code only if nonHydrostatic=T
3430 - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
3431 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
3432 => Update output of experiment seaice_obcs
3433 - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
3434 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
3435 - fix restart for useOBCSprescribe + useEXF
3436 o pkg ctrl
3437 - make obcs as control parameter work also with useSingleCPUio
3438 - replace a few sny and snx by Ny and Nx to be consistent with
3439 ctrl_set_globfld_x/yz.F
3440 o pkg seaice
3441 - re-introduce global field frWtrAtm for the case of
3442 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
3443 - catch the case of an empty filename in seaice_cost_init_fixed.F
3444 o pkg ecco:
3445 - small bug fixes in the_main_loop
3446 . fix order of monitor arguments
3447 . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
3448 . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
3449 that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
3450 - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
3451 imbalance diagnostics for wmean_h/sflux = 0
3452 - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
3453 - catch the case of empty filenames in ecco_cost_init_fixed.F
3454 and ecco_readparms.F
3455 - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
3456 to make this statement meaningfull in ecco_cost_weights.F
3457 o pkg zonal_filt:
3458 - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
3459 - when using rStar, filter uVel*hFacW instead of uVel
3460 (tested without topography: fix a Pb of growing instability with NLFS)
3461 o pkg/aim/thsice:
3462 -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
3463 (works as SST restoring)
3464 o pkg/thsice:
3465 -add specific parameter for salt restoring in slab mixed-layer
3466 (by default equal to the temperature restoring)
3467
3468 checkpoint61v (2009/09/21)
3469 o pkg/kpp:
3470 -add double diffusive contributions as a hack, turned off by default
3471 for now, and the code can be excluded with a CPP-flag
3472 EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
3473 -add a verification experiments to "vermix" to test this code
3474 o pkg/mom_common:
3475 Move computation of length scales to mom_init_fixed.F (avoid recomputation
3476 at each time-steps*levels).
3477 o pkg/layers:
3478 Created a new package for computing volume fluxes in temperature or
3479 [not yet implemented] density layers, e.g. for calculating residual
3480 overturning circulations.
3481 o pkg/diagnostics:
3482 implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
3483 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
3484 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
3485 To avoid mixing type (RS/RL) of input/output array argument,
3486 replace single mixed-type array with a pair from each type (RS/RL).
3487 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
3488 is now implemented for all pkgs (previously only done for the main pickup)
3489
3490 checkpoint61u (2009/08/25)
3491 o pkg/obcs:
3492 - change OB?eta from _RS to _RL and put them into a separate commen block
3493 - add code to read OB?eta from a file via obcs_prescribe_read: the code
3494 compiles and does not destroy any other experiments, the data is read
3495 properly, but the code is not tested in actual applications
3496 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
3497 create a meaningful unit attribute for the time coordinate variable
3498 o pkg/ebm: add plenty of missing "_d 0" ;
3499 update results of experiment global_ocean_ebm (fwd + adjoint tests)
3500 Notes: several pieces of code only works for (very) specific set up
3501 (domain size, lat range, etc ...); should be documented & stop if one
3502 of those assumptions is not meet.
3503 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
3504 update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
3505 and offline_exf_seaice (seaicetd + adjoint).
3506 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
3507 update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
3508 seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
3509 o few changes to pass when compiling with strick checking of arguments
3510 across S/R (allow to find few bugs in S/R calls).
3511 o pkg/seaice:
3512 - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
3513 2d-fields, for slightly better performance
3514
3515 checkpoint61t (2009/07/22)
3516 o pkg/seaice:
3517 - remove unused variables in seaice_evp
3518 - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
3519 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
3520 named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
3521 each processor opens a different file (a fix from Matt).
3522 o cg2d:
3523 use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
3524 this reduces number of EXCH calls by 2 when using exch2.
3525 For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
3526 directives and missing simple EXCH (exch_s3d_rx) adjoint code.
3527 o pkg/thsice:
3528 add code for Near Infra-Red albedo (from Jeff)
3529 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
3530 o ini_model_io:
3531 move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
3532 MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
3533 to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
3534
3535 checkpoint61s (2009/06/30)
3536 o pkg/exch2 (exch2_rxN_cube*):
3537 remove last BARRIER (no need to synchronise after getting data from shared
3538 buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
3539 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
3540 and generate new output (for the 2 tests) using default rotationPeriod.
3541 o pkg/exch2:
3542 - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
3543 (was already the case with AUTODIFF_EXCH2 defined)
3544 - add bj in exch2 arrays and S/R.
3545 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
3546 MLAdjust to exch2 (identical results except with MPI -> truncation diff);
3547 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
3548 - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
3549 GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
3550 - verification experiment natl_box.longstep
3551 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
3552 allow different versions of ifort (8 or 9) and different versions
3553 of mpi (mpich or mpich2) to be used with the same optfile.
3554 requires to load a netcdf module and set MPI_INC_DIR (see comments inside
3555 optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
3556 o pkg/seaice:
3557 fix previous modif (3-level field removed) for old-pickup reading
3558
3559 checkpoint61r (2009/06/25)
3560 o pkg/seaice:
3561 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
3562 1. introduce fields for time step (N-1)
3563 2. do not use levels 2 and 3 anymore (but keep them)
3564 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
3565 includes changes to pkg/thsice/thsice_get_velocity.F,
3566 model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
3567 pkg/obcs/obcs_apply_uvice.F.
3568 - completely remove code for leap-frog time stepping for second order
3569 advection
3570 - adjusted adjoint accordingly;
3571 gradient checks have improved by an order of magnitude!
3572
3573 checkpoint61q (2009/06/22)
3574 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
3575 - the boundary conditions along open boundaries are unclear, because the
3576 associated masks are set to zero and are thus treated as closed when
3577 applying the slip-boundary conditions.
3578 - move initialisation of grid variables from seaice_init_varia to _fixed
3579 o adding doc/diags_changes.txt
3580 o model/src:
3581 do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
3582 to avoid "_diags" naming if no relation to pkg/diagnostics.
3583 ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
3584 file and only call PLOT_FIELD_XYZ if debugMode=T.
3585 remove few PLOT_FIELD_XY calls outside initialisation.
3586 remove few unnecessary BARRIER.
3587 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
3588 of salt_plume package in Southern Ocean
3589 o pkg/thsice:
3590 - fix hOceMxL in overlap (needed for sea-ice advection);
3591 update output of experiment global_ocean.cs32x15.icedyn.
3592 o pkg/seaice:
3593 - make the (placeholder-)tracer IceAge a little more meaningful
3594 by avoiding ridging of age due to convergent ice flow
3595 - add diagnostics for surface temperature, atmospheric and oceanic
3596 heat flux, and atmospheric and oceanic ice growth
3597
3598 checkpoint61p (2009/06/10)
3599 o eesupp (global_max & global_sum):
3600 - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
3601 - remove starting & endding barrier (no longer needed)
3602 o pkg/mdsio, writelocal:
3603 works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
3604 (remove the STOP): uses shared buffer IO to store data from all threads
3605 and then let master-thread write nThreads tiles.
3606 o pkg/mdsio (read/write field):
3607 - tiled IO done in 1 piece (all levels at a time);
3608 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
3609 - multi-threaded: allow to read/write local (non-shared) array
3610 (was already working with singleCpuIO ; now works also without);
3611 => no longer needs barrier call after reading a file (added inside
3612 mds_read/write field).
3613 - move barrier calls outside gather/scatter_2d to mds_read/write_field
3614 o pkg/obcs/exf
3615 - exf_getffieldrec.F: add a few ". _d 0" and
3616 add code to catch the case fldperiod = 0.
3617 - obcs_precribe_read.F: change if statements so that they match
3618 the variable type (_RL)
3619 - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
3620 exf_iprec) as part of namelist EXF_NML_01
3621 o pkg/mdsio:
3622 - read/write tiled (local) files: read/write 1-level tile chunk at a time
3623 (instead of segment of length sNx); expected to speed up tiled IO.
3624 o pkg/exch2:
3625 - take buffer copy from/to array out of S/R exch2_send/recv into new
3626 S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
3627 (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
3628 - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
3629 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
3630 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
3631 including Topology header file (and common blocks).
3632 - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
3633 remove 2nd exch call in exch2_s3d_rx (no longer needed).
3634 - document S/R arg. list (+ update some comments)
3635 o pkg/seaice:
3636 - added SEAICE_CLIM_AIR code, which permits modulation of surface air
3637 temperature and humidity over sea ice based on climatological values.
3638 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
3639 of LSR (this change is expected to change the results slightly because now
3640 it uses slightly difference moduli from the second last LSR solution, but
3641 that is more consistent with the stress computations; this part of the code
3642 is not tested in the verification experiments)
3643 - fix diagnostics for flux of ice in case of B-grid
3644 - turn strain rates eij and press into global fields within global
3645 common block in SEAICE.h for more straighforward diagnostics
3646 - fix diagnostics for principal stress components, press, zeta, eta
3647 to give something meaning full
3648 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
3649 new output (all 4 tests) using default rotationPeriod.
3650 o pkg KPP:
3651 - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
3652 - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
3653 and normal grid from 1 to Nr)
3654 o Fix computations of L4rdt in mom_calc_visc.F
3655 o eesupp:
3656 new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
3657 should be called before a "stop" if we know that all process are going
3658 to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
3659
3660 checkpoint61o (2009/05/26)
3661 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
3662 o model/src/ini_curvilinear_grid.F:
3663 compute angleSin/CosC when they are not read from a file
3664 o pkg/seaice:
3665 add pseudo time stepping for LSOR
3666 o pkg/exch2:
3667 temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
3668 o pkg/seaice:
3669 Adding separate sea ice albedo, drag coefficients, and HO in Southern
3670 Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
3671 o SingleCpuIO:
3672 fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
3673 o pkg/seaice:
3674 put exchanged variable in (local) common block for MPI+Multi-Threads
3675 to work (necessary with exch1, and for now with exch2 too).
3676 o verification: to get more experiments tested with mpi, mth and mpi+mth,
3677 change tiling of:
3678 aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
3679 hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
3680 update output of exp:
3681 exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
3682 tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
3683 + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
3684 (note: output.txt generated on faulks using only 1 tile)
3685 o eesupp & mdsio (SingleCpuIO):
3686 - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
3687 parameter "W2_useE2ioLayOut" (read from file "data.exch2").
3688 Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
3689 - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
3690 - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
3691 gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
3692 o pkg/exch2:
3693 - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
3694 read parameter file "data.exch2" if it exists; otherwise try default regular
3695 cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
3696 - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
3697 with new code (not to be used, just as a backup solution).
3698 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
3699 in utils/exch2/input.
3700
3701 checkpoint61n (2009/05/12)
3702 o eesupp & mdsio (SingleCpuIO):
3703 - move mapping to global io-buffer inside gather_2d/scater_2d: this save
3704 memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
3705 receive real*4 array (instead of real*8) to read/write 32.bit files.
3706 (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
3707 and remove new mapping S/R)
3708 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
3709 - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
3710 xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
3711 when using exch2. Add S/R to map global io-buffer to global model array.
3712 - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
3713
3714 checkpoint61m (2009/04/29)
3715 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
3716 and add 3 other S/R for other types (R4,R8,RS).
3717 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
3718 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
3719 - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
3720 - reduce number of macro definitions (keep only those which are used);
3721 can always call directly the corrresponding S/R if needed.
3722 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
3723 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
3724 Fixed wrong type of arg in:
3725 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
3726 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
3727 To fix: global_sum of var in common block is wrong (multi-threaded) in:
3728 dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
3729 To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
3730 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
3731 "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
3732 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
3733 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
3734 edges are closed (zero depth); might happen with "blank tiles";
3735 for now, disabled if using OBCS.
3736 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
3737 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
3738 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
3739 to reduce length of 1.D array print in STDOUT.
3740 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
3741 + use 48 tiles (16x8): this will allow to test "blank tiles".
3742 o start to test MPI + multi-threaded (change testreport to skip tests
3743 where number of tiles do not match).
3744 o genmake2: add option "-omp" to turn on Open-MP ;
3745 passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
3746 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
3747 and keep the original tile numbering. Note: compatible with old
3748 W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
3749
3750 checkpoint61l (2009/04/07)
3751 o Overlaps had been forgotten in calculating ijk keys : fixed
3752 o fix cyrus makedepend for gcc 4.4
3753 o experiment fizhi-cs-aqualev20:
3754 switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
3755 and generate new output. Note: new output is much closer to the old
3756 one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
3757 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
3758 o pkg/fizhi:
3759 - change to avoid indices going deliberately over array-bounds
3760 - remove unnecessary MPI stuff
3761 - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
3762 - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
3763 does not go over array-bounds and therefore returns reliable output.
3764 - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
3765 this S/R has 4 output arguments, which are used inside "get_alarm";
3766 when it is called with the same variable "ndum" in place of several
3767 output arguments, this produces weird side effect inside "get_alarm"
3768 (e.g., datein=dates(n) is overwritten by timein=times(n) since both
3769 datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
3770 address) and produces error.
3771 o tools/gemake2: (March 27-29 2009)
3772 with option "-mpi": link *_mpi files from "MODS" dir (this is what
3773 testreport does).
3774 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
3775 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
3776 update lab_sea.lsr & lab_sea.salt_plume results
3777 o pkg/seaice:
3778 Major overhaul of the LSOR solver: change discretization from original
3779 finite differences to finite volume. The old routine is still in the
3780 file seaice_lsr.F and can be turned on with the CPP-flag
3781 SEAICE_OLD_AND_BAD_DISCRETIZATION
3782 Along with this change, the discretization of the strain rates is changed.
3783 The same flag turns on the old discretization in seaice_calc_strainrates.F
3784 All verification experiments with seaice are affected (except for
3785 seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
3786 results by setting the above flag.
3787 Further changes involve changes in defaults:
3788 - ALLOW_FLOODING is defined and turned on by default
3789 - SEAICEadvSnow = .true. is now the default
3790 - SEAICEadvSalt = .true. is now the default
3791 - SEAICEadvAge = .true. is now the default
3792 - SEAICE_clipVelocities = .false. is now the default
3793 (as per J. Zhang's recommendation)
3794 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
3795 is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
3796 - seaice_growth: replace computation of UG by a simple copy from wspeed
3797
3798 checkpoint61k (2009/03/18)
3799 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
3800 seaice_lsr: fixed a few metric terms,
3801 affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
3802 add more debugging diagnostics
3803 seaice_evp: removed superfluous many metric terms of FV discretization
3804 of stress divergence
3805 affects lab_sea, lab_sea.hb87
3806 seaice_ocean_stress: removed superfluous many metric terms of FV discretization
3807 of stress divergence for non-evp solver
3808 (this part is not tested anywhere)
3809 seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
3810 they were effectively only half slip
3811 affects lab_sea.hb87
3812 updated all relevant verification experiments (except lab_sea//output_adm.txt
3813 which was left over, but fails at level 7 & 6)
3814
3815 checkpoint61j (2009/03/17)
3816 o pkg/seaice: turn a few hard wired parameters into run time parameters
3817 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
3818 time in seconds as promised by the usints in seaice_monitor and exf_monitor
3819 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
3820 that are not cubed-sphere grids
3821 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
3822 o pkg/ctrl:
3823 fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
3824 o non-hydrostatic (calc_gw.F):
3825 fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
3826 update output of exp. global_ocean.cs32x15.viscA4
3827 o remove backward compatibility for thetaMin,phiMin
3828 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
3829 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
3830 interpolated wind field not only for curvilineargrid=.true., but also
3831 for a rotated grid (rotateGrid=.true.)
3832 o pkg/exf: add capability to bypass interpolation for runoff
3833 by setting yet another CPP-flag
3834 o eesupp/src, B-grid exchange:
3835 add simple (6 tiles, non MPI) CS exch + standard interface S/R.
3836 o autodiff
3837 new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
3838 allows to switch to single-prec common blocks;
3839 corresponding switch occurs in tamc.h, integer isbyte
3840 TAF store directivs "byte" and "kind" seem equivalent;
3841 Most tamc.h have been updated correspondingly.
3842
3843 checkpoint61i (2009/02/13)
3844 o autodiff:
3845 fix autodiff_sore/_restore indices for obcs
3846 (spotted by I. Hoteit, M. Mazloff)
3847 o pkg/autodiff, pkg/ctrl:
3848 Add flag to reduce all tapelev I/O to single-prec.
3849 In data.ctrl set
3850 doSinglePrecTapelev = .TRUE.
3851 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
3852 check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
3853 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
3854 real fresh water flux (not yet)
3855 o pkg/mdsio & rw:
3856 - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
3857 - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
3858 o pkg/flt:
3859 - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
3860 init_fixed & ini_varia.
3861 - clean-up & simplify linear interpolation S/R:
3862 move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
3863 - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
3864 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
3865 - add vert. coordinate & horiz. indices to output files.
3866 - change vertical position in initial condition, from index to depth [m].
3867 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
3868 (easier to get to a curvilinear grid) ; delX,delY no longer used.
3869 o pkg/ggl90: a few modifications:
3870 - fix bottom boundary condition, and interpolation of KappaE
3871 near top and bottom
3872 - use same set of viscosity/diffusivity for TKE/momnetum/tracer
3873 - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
3874 - add a few options for mixing-length upper limit (--> mxlMaxFlag)
3875 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
3876 (maintain temporary backward compatibility, until next checkpoint)
3877
3878 checkpoint61h (2009/01/27)
3879 o pkg/diagnostics with "periodic averaging diagnostics":
3880 fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
3881 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
3882 o pkg/obcs: fix loop ranges for balancing code
3883 o pkg/flt:
3884 - improve criteria for finding which tile owns a float.
3885 - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
3886 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
3887 aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
3888 with ocean biogeo)
3889 o pkg/flt:
3890 - do some cleaning and fix the restart ;
3891 - add output.txt in flt_example/results to get this pkg tested.
3892 o genmake2: add an EXTENDED_SRC option and flag.
3893 for now, cannot be turned on on command line (only through genmake_local)
3894 o pkg/mdsio: read/write vector:
3895 - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
3896 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
3897 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
3898 - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
3899 (drop to 4 digits matching for grad). But this test does not look very
3900 reliable (was already failling on eddy, fc5, at 6.digits). Update output.
3901
3902 checkpoint61g (2008/12/29)
3903 o pkg/flt:
3904 - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
3905 + make OPTIONS file more standard.
3906 - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
3907 - fix _BYTESWAPIO CPP-Flag
3908 - standard reading of file-parameter "data.flt"
3909 - fix argument list of S/R FLT_RESTART
3910 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
3911 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
3912 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
3913 a still unfixed compiler/optimization bug
3914
3915 checkpoint61f (2008/11/21)
3916 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
3917 update results of global_ocean.cs32x15.icedyn test.
3918 o move getcon.F from model/src to pkg/fizhi.
3919 o pkg/exf: add parameter for extrapolation of temp up to the surface
3920 and option to prevent negative evap (in bulk_largeyeager04 only).
3921 o Prather Advection scheme: fix tracer conservation for divergent flow
3922 (e.g., when using NonLin Free-Surface).
3923 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
3924 o gmredi (Visbeck-variable-K):
3925 - add more parameters to Visbeck-variable-K.
3926 - use a 5 points average for dSigmaR in Visbeck-K calculation
3927 (more "homogenous": same stencil and same weights as in dSigmaH)
3928 - update output of ideal_2D_oce experiment.
3929 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
3930 (#undef REAL4_IS_SLOW)
3931 - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
3932 coordinate variable
3933 - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
3934 (surface forcing fields), removes some of the functionality
3935 - model/src/write_grid.F: write _RS variables as RS-netcdf variables
3936 - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
3937 probably not all: copy _RS surface flux fields to RL field before
3938 calling DIAGNOSTICS_FILL
3939 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
3940 real*4 (CALL EXCH_*_RS) versions.
3941 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
3942 (generate new output).
3943
3944 checkpoint61e (2008/10/23)
3945 o gmredi (Visbeck-variable-K):
3946 - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
3947 - change computation of Visbeck-K where Slope > Smax :
3948 now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
3949 previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
3950 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
3951 to be the same as with Z-coord. (i.e., m/s & no-units respectively).
3952 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
3953 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
3954 does not become too large (to avoid precision problems in implicit-diffusion
3955 solver); update ideal_2D_oce output.
3956 o pkg ggl90:
3957 - in ggl90_cal.F: compute only one set of visc/diff, used to
3958 step forward TKE/T/S/momentum
3959 - default value of GGL90viscMax/GGL90diffMax larger and equal (to
3960 have Prandlt =1)
3961 o gmredi (fm07):
3962 - add lower limit on Transition layer thickness + lower limit on 1/lambda
3963 - allow to set few more params from data.gmredi
3964 o pkg ggl90:
3965 - add missing sqrt(2) factor in computation of mixing length
3966 scale in ggl90_calc.F
3967 (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
3968
3969 checkpoint61d (2008/09/25)
3970 o adjoint modifs
3971 - adapt to new field rhoInSitu
3972 - allow to revert from StoreDynVars2D, StoreDynVars3D
3973 to individual fields
3974 (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
3975 o store 3-D (in-situ) density in commom block (DYNVARS.h)
3976 - save 1 rho computation.
3977 - no longer modify T & S inland when using down_slope pkg.
3978 o gad_som : allow to switch to SOM advection for T & S without corresponding
3979 pickup files (using new S/R: MDS_CHECK4FILE).
3980 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
3981 (for useSingleCpuIO to work in multi-threaded)
3982 o pkg/shelfice:
3983 - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
3984 with SHELFICEtopoFile in data.shelfice
3985 - move code for reading ice shelf topography and modifying hFacC into separate
3986 subroutines of the shelfice package
3987 - separate initialisation of "fixed" and "variable" variables
3988 - kTopC is not (yet) replaced by kSurfC, although this is possible
3989 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
3990 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
3991 and rename:
3992 ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
3993 ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
3994 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
3995
3996 checkpoint61c (2008/08/30)
3997 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
3998 to add mass source/sink of fluid in the interior (3-D generalisation
3999 of oceanic real-fresh water flux).
4000 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
4001 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
4002 o new pkg: down_slope
4003 density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
4004 - presently, modify T & S inland (dwnslp_calc_rho.F).
4005 can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
4006 - implementation for ocean in P-coords not tested.
4007 - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
4008 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
4009 (to facilitate conversion of oceanic pkg to p-coordinate).
4010 o change FIND_RHO to FIND_RHO_2D :
4011 pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
4012 o new pkg: cheapaml
4013
4014 checkpoint61b (2008/08/05)
4015 o exch2:
4016 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
4017 - no longer depend on the order sequence (N,S,E,W).
4018 - 3rd exchange no longer needed (tested with 24 tiles).
4019 - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
4020 - exch_UV_A-grid readily available (but not yet tested).
4021 comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
4022 (both are no longer needed) in exch_uv: no effect in forward run; but
4023 get truncation error differences with adjoint exch.
4024 o exch2:
4025 - change index-bounds storage (moved from target to local tile,
4026 more intuitive this way) ; rename/remove some variables.
4027 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
4028
4029 checkpoint61a (2008/07/29)
4030 o exch2/matlab-topology-generator:
4031 fix bug in index bounds for N-S internal exchange (hard to tell if this
4032 had any effect on the solution).
4033 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
4034 is exceeded
4035 o testreport: modify syntax of awk, so that it works also with
4036 awk, and not only with nawk and gawk
4037
4038 checkpoint61 (2008/06/24)
4039 o autodiff
4040 Change default for TAF usage by removing argument '-nonew_arg'
4041 This changes TAF subroutine argument list (ordering of active var.)
4042 Omission of this flag leads to incompatibility w.r.t. TAMC
4043 To restore TAMC-compatibility, need following modifs:
4044 * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
4045 * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
4046 Tested TAF version is 1.9.22
4047 N.B.: exch2 hand-written adjoint code currently not TAMC compatible
4048
4049 checkpoint60 (2008/06/19)
4050 --->>> This is the last checkpoint for which generating the adjoint
4051 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
4052 --->>> by default.
4053 --->>> Future checkpoints will ommit this flag by default.
4054 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
4055 o pkg/grdchk: Add gradient check to etan0 perturbations.
4056 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
4057 o pkg/autodiff: more flexibility in zeroadj.
4058 model/src: modifying do_oceanic_phys.F accordingly.
4059 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
4060 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
4061 special setup of gmredi for which the adjoint is stable
4062 enough for parameter optimization.
4063 o bridging the gap between eddy stress and GM.
4064 -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
4065 along with a change in CPP option (now ALLOW_EDDYPSI).
4066 -> when using GM w/ GM_AdvForm:
4067 The total eddy streamfunction (Psi = eddyPsi + K x Slope)
4068 is applied either in the tracer Eq. or in momentum Eq.
4069 depending on data.gmredi (intro. GM_InMomAsStress).
4070 -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
4071 The key modifications are in model/src/taueddy_external_forcing.F
4072 pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
4073
4074 checkpoint59r (2008/05/29)
4075 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
4076 from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
4077 fix option to read coriolis(@ cell-corner) from files with CS-grid.
4078 o pkg/mnc: add some attributes to standard 1D-coordinate variables
4079 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
4080 mass points, when using mnc for output
4081 - add runtime parameter (missing_value, missing_value_int) to override
4082 default (which is the value of getcon('UNDEF'))
4083 o pkg/mnc: prepare mnc for the actual use of missing values with the
4084 diagnostics package: small fix in mnc_cw_readwrite.template and more
4085 initialisation of never used fields
4086 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
4087 versions
4088 o pkg/thsice/thsice_ini_vars.F added default initial values so that
4089 thermodynamics sea ice solver does not blow up when some initial fields
4090 are missing.
4091 o move from external_forcing_surf.F to ini_forcing.F
4092 the p-coord. hack consisting in using pLoad to set phi0surf ;
4093 update output of tutorial_global_oce_in_p (affected @ truncation level).
4094 o Freshen up a bit hs94.1x64x5, notably:
4095 remove rotationPeriod and tRef=5*0. (adjoint only), and add
4096 exactConserv=.TRUE.
4097 o pkg/generic_advdiff:
4098 change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
4099 applies to files where Temperature & Salinity 2nd Order moments are used.
4100 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
4101 this uses a dynamically allocated internal state data structure
4102 (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
4103 and requires a fortran 90 compiler
4104
4105 checkpoint59q (2008/05/06)
4106 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
4107 (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
4108 o Refresh tutorial_global_oce_biogeo, notably:
4109 - change bathymetry (put back seamounts in ACC, use hFacs)
4110 - change EOS (POLY3 --> JMD95Z)
4111 - use Bryan-Lewis vertical diffusivity
4112 - use multidimensional advection
4113 - remove old virtual virtual in dic pkg, now done through ptracer pkg
4114 - change a couple of parameters in dic pkg
4115 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
4116 o pkg/obcs: change default to OBCSfixTopo = .true.,
4117 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
4118 - replace "debugMode" with "debugLevel .GE. debLevB"
4119 o implementation of TAF directives for gchem,cfc,dic
4120 o remove "exp5" (replaced by tutorial_deep_convection).
4121 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
4122 this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
4123 the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
4124 --> changes results in exp4, seaice_obcs
4125 o tutorial_deep_convection :
4126 update the set-up and increase resolution and domain size ; start
4127 from pseudo initial conditions = output at t=120mn in order to see
4128 something happening when running testreport.
4129 o pkg/seaice: add os7mp as an advection scheme
4130 add check for advection schemes
4131 add a flag for restoring T and S underneath sea ice
4132 o pkg/my82: add netcdf-support and diagnostics
4133 o thsice pkg:
4134 - Now hsMax limits snow height by turning it into ice following
4135 flooding scheme (and now conserving energy)
4136 - Slight rewriting of the formula in thsice_calc_thick.F
4137 - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
4138 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
4139
4140 checkpoint59p (2008/04/10)
4141 o gchem / dic / cfc :
4142 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
4143 - add new parameter files: "data.dic" & "data.cfc" ;
4144 - various re-arrangement in initialisation & header file ;
4145 - fix tutorial_global_oce_biogeo for multi-threaded test.
4146 o pkg/dic: test for "pickup_dic" file when restarting ;
4147 if no pickup-file, can restart with a re-initialised pH (same as it did
4148 before) providing pickupStrictlyMatch is set to False.
4149 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
4150 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
4151 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
4152 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
4153 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
4154 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
4155 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
4156 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
4157 scheme to use for vorticty-term ;
4158 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
4159 (with default selectVortScheme, return to original discretisation)
4160 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
4161 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
4162 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
4163 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
4164 also fix diagnostics VISCAHW & VISCA4W.
4165
4166 checkpoint59o (2008/03/07)
4167 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
4168 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
4169 move a few statemens out the main loop into separate loops
4170 o pkg/shelfice:
4171 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
4172 (kg/m^2/s), does not break tests, because in verification/isomip,
4173 rhoConstFresh=rhoConst (by accident)
4174 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
4175 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
4176 new file model/src/seawater.F, so that they are available for all pkgs.
4177 - convert potential temperature into in-situ temperature. This changes the
4178 isomip tests => update tests
4179 o add a flag writePickupAtEnd (default=true) to be able to suppress
4180 writing a pickup at the last timestep
4181 o tools/mpack-1.6 :
4182 - disable automake (not working) and autoconf (not needed).
4183 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
4184 also cleaner with much less compilation warnings.
4185 o pkg/profiles:
4186 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
4187 (for "less than 32 characters name" compiler requirement)
4188 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
4189 conditions that have a different sampling frequency than S/T/U/V obcs
4190 o pkg/diagnostics (stats-diags):
4191 - fix global Min/Max in case 1 processor get only empty tiles
4192 o genmake2: replace (4 times)
4193 make genmake_tc_1.o >> genmake_warnings 2>&1
4194 with
4195 COMM="$CC $CFLAGS -c genmake_tc_1.c"
4196 echo $COMM >> genmake_warnings
4197 $COMM >> genmake_warnings 2>&1
4198 to make genmake2 always see the value of CC as specified in the optfile.
4199 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
4200 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
4201 - modify verification advect_cs test to test SOM-advection on CS-grid.
4202 o pkg/ctrl:
4203 - Rewrite of ctrl_map_ini_ecco.F,
4204 introducing a generic routine (ctrl_map_ini_gen.F).
4205 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
4206
4207 checkpoint59n (2008/02/09)
4208 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
4209 number in dedicate array "hdiag":
4210 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
4211 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
4212 - many small changes (integer format) for large number of diagnostics
4213 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
4214 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
4215 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
4216 usingSphericalGrid, this allows to define the rotated grid coordinates
4217 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
4218 geographical coordinates according to the inverse of the rotation defined
4219 by the Euler angles, so that Coriolis parameter and online-interpolation by
4220 exf works with the geographical coordinates on XC/YC/XG/YG.
4221 Naturally, this feature does not work with all packages, so some
4222 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
4223 profiles), because there the coordinates are assumed to be regular
4224 spherical grid coordinates.
4225 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
4226 - introduce isopycnal diffusion coefficient control.
4227 o tools/adjoint_options:
4228 - additional control vector components.
4229 o pkg/mnc: have mnc create marginally meaning full coordinate variables
4230 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
4231 o pkg/mypackage:
4232 - add example of read/write pickup for state-var ;
4233 - add entry points to the main code for state-vars diags & write-pickup.
4234 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
4235 transitions for useExfYearlyFields
4236 - add new subroutine that determines the file to read from for
4237 use*YearlyFields = .TRUE. and .FALSE.
4238 - add a verification experiment to global_with_exf that tests
4239 useExfYearlyFields with USE_EXF_INTERPOLATION defined
4240 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
4241 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
4242 subroutines (which could be generated from a template, because they are
4243 almost identical), for now they are included in obcs_prescribe_read.F for
4244 simplicity
4245 o pkg/exf:
4246 - add a little more diagnostic to exf_interp_read (in analogy to
4247 mds_read_field, can be turned off with debugLevel < debugLevA=1)
4248 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
4249 ugly but fast by unrolling short inner loops, inserting a unroll=8
4250 directive in routine lagran, and splitting a loop and making do while the
4251 outermost loop (the latter requires the intoduction of index arrays)
4252 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
4253 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
4254 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
4255 o verification/seaice_obcs: updated for restart test and latest options
4256 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
4257 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
4258 for now this is only available for the C-grid code and also within
4259 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
4260
4261 checkpoint59m (2008/01/14)
4262 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
4263 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
4264 o gad_som : fix flux output (& diagnostics) to have same units as other
4265 advection scheme fluxes (was previously multiplied by deltaT).
4266 o added verification/seaice_obcs both to test seaice open boundaries
4267 and to provide an example matlab scrpt for generating them
4268 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
4269 o pkg/salt_plume: clean up salt_plume_frac.F to
4270 remove redundancy in PlumeMethod 1 and 4
4271 o pkg/kpp: added saltplume diagnostics
4272 o pkg/obcs and pkg/seaice:
4273 - do not set uice and vice to zero when OB*icefile are unspecified
4274 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
4275 - moved seaice tracer obcs after call to seaice_growth
4276 o pkg/salt_plume: added various options for salt plume depth
4277 criterion and for vertical distribution of the salt
4278
4279 checkpoint59l (2007/12/18)
4280 o pkg/ptracers: new version of ptracers pickup:
4281 read meta file and write only fields which are needed to restart.
4282 ( same logic as main pickup file ; also using pickupStrictlyMatch )
4283 o pkg/seaice:
4284 - add timescale for melting due to warm mixed layer as a means of
4285 setting SEAICE_availHeatFrac more conveniently
4286 - add a CPP-flag/runtime parameter check for flooding algorithm
4287 - reformulated availHeat in seaice_growth.F to be independent of AREA
4288 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
4289 unit changes
4290 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
4291 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
4292 SX vector computer.
4293 o pkg/seaice:
4294 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
4295 seaice forcing fields can now be read only through pkg/exf
4296 - removed some unused halos
4297 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
4298 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
4299 or U/VICE from U/VWIND before computing U/VSTRESS
4300
4301 checkpoint59k (2007/11/30)
4302 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
4303 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
4304 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
4305 all experiments pass when compile with un-initialised var. checking option.
4306 o added pkg/salt_plume
4307 o script to test restart (for now, in MITgcm_contrib/jmc_script)
4308 o pkg/seaice: new read/write pickup version.
4309 read meta file and write only fields which are needed to restart.
4310 ( same logic as main pickup file ; also using pickupStrictlyMatch )
4311 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
4312 o lab_sea.hb87: modify the domain & update output.hb87.txt :
4313 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
4314 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
4315 process. Fixed here by closing the domain at the Northern boundary.
4316 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
4317 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
4318 a set of consecutive levels in/from a 3-D array.
4319 o pkg/ptracers:
4320 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
4321 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
4322
4323 checkpoint59j (2007/11/09)
4324 o in pkgs: dic, obcs, offline, rbcs:
4325 standard way to compute coeff. for time interpolation between 2 time reccords
4326 which retains full precision (& make results less dependent on compiler).
4327 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
4328 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
4329 packages instead of reading ice cover and wind speed separately
4330 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
4331 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
4332 to allow to compile customized code before the update)
4333 o cleaning-up:
4334 - fix CPP instruction syntax in pkg/obcs
4335 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
4336 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
4337 - fix some threads issue in IO parts.
4338 o pkg/dic:
4339 - add tons of "_d 0" (--> much better testreports !)
4340 and then update outputs of tutorial_global_oce_biogeo
4341 o pkg/mom_fluxform:
4342 add a special version of momentum advection intended to conserve momentum
4343 next to a bathymetry step or a coastline edge. (default = off = #undef)
4344 o new read/write pickup version:
4345 - for now, only implemented for main (mdsio) pickup file.
4346 - write out only what is needed to restart; merge pickup_nh , pickup_ph
4347 and main pickup together.
4348 - read meta file; read only what is needed to restart; stop if a field
4349 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
4350 if it make sense (even if the restart is not perfect).
4351 - if no meta file, assume that pickup to read corresponds exactly to
4352 a pickup that would currently be written.
4353 - read pickup written in the old format (until checkpoint59i) if it
4354 recognizes an old meta file (no field-list).
4355 - add a meta file in exp. which starts from a pickup: 2 cases:
4356 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
4357 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
4358 b) a meta file describing the content of the associated pickup file
4359 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
4360 o pkg/mdsio & pkg/rw:
4361 - new routine to read a meta file ; new set of routine to read
4362 Multiple-fields file (with meta file).
4363 o added open boundary conditions capability for seaice
4364 HSNOW, HSALT, UICE, and VICE
4365
4366 checkpoint59i (2007/10/21)
4367 o adjoint:
4368 * fix multiDimAdvection adjoint
4369 (partial recomputation problem by TAF for fVerT(:,:,kDown)
4370 and comlev1 size definition (maxpass vs. max. number of tracers)
4371 * verification/global_ocean.90x45x15 adjoint now tests
4372 NLFS and multiDimAdvection using DST3 (=30)
4373 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
4374 o pkg/kpp: add "_d 0" to real constant (if missing);
4375 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
4376 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
4377 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
4378 for internal parameters related to restart process (formerly from PARAMS.h)
4379 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
4380 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
4381 as argument. (only atm2d & obcs write_pickup have not yet been updated)
4382 o pkg/monitor:
4383 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
4384 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
4385 - account for deep Atmosphere factor and density factor (anelastic)
4386 o added open boundary conditions capability for seaice HEFF and AREA
4387 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
4388 thermodynamics
4389 - requires a little reorganization, which affects the testreport results
4390 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
4391 so that now the conservative form is tested
4392 - add a few comments
4393 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
4394 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
4395 o add new diagnostics to seaice: advective, diffusive fluxes (only for
4396 multidim-advection, for scheme 2 they are not filled) and transports,
4397 thermodynamic growth rates
4398 o change units of EmPmR (inside the code, + within coupling interface)
4399 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
4400 Affects results @ truncation level (cg2d match) and update output of
4401 experiments: lab_sea(6), global_ocean.90x40x15(10),
4402 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
4403 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
4404 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
4405 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
4406
4407 checkpoint59h (2007/09/29)
4408 o pkg/exf:
4409 - improve vectorization by moving if-statement out of loops in
4410 exf_mapfields, exf_radiation
4411 - exf_bulkformulae.F: introduce 2D fields and vectorize code
4412 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
4413 o testreport:
4414 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
4415 monitor & update offline_exf_seaice exp. output.
4416 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
4417 o pkg/seaice:
4418 - bug fix in the evp solver: boundary conditions were affected be
4419 masking of zMax/zMin (changes results)
4420 - minor bug fix in boundary conditions in seaice_calc_strainrates
4421 (changes results for no_slip)
4422 - seaice_lsr.F: make interpolation of eta dependent on boundaries
4423 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
4424 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
4425 stress formulation and no-slip boundary conditions
4426 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
4427 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
4428 o pkg/seaice: a first HSALT time stepping equation has been checked in
4429 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
4430 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
4431 without requiring DO-IF statements
4432 o pkg/thsice:
4433 use continuous power-law function for partition of energy between lateral
4434 melting/freezing and thinning/thickening ; old code using step function
4435 still available with #undef THSICE_FRACEN_POWERLAW
4436 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
4437 o testreport: change AD testing : check against results/output_adm.txt
4438 using same scripts as for forward test.
4439
4440 checkpoint59g (2007/09/17)
4441 o adjoint testing: in preparation for changing testreport:
4442 - output format: cost and grad written on separated lines
4443 - ad output results in directory "results" (instead of "results_ad")
4444 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
4445 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
4446 o pkg/ecco: allow user defined cost function contributions
4447 o testreport:
4448 Allow to choose (per experiment) the list of tested output variables
4449 and the main variable (used to issue a pass/FAIL ) ;
4450 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
4451 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
4452 Also modify printing of summary:
4453 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
4454 b) echo the list of tested variables in the individual summary.txt of
4455 each experiment.
4456 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
4457 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
4458 (but still depend on the tile decompostion of the domain).
4459 o pkg/seaice: change a discretization detail to make the B-grid code
4460 "more symmetric". This change is likely to remove all "ridges/leads" that
4461 where quasi-aligned with the grid in B-grid solutions. It may also be
4462 the solution to the stress coupling issues with the B-grid.
4463 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
4464 remove .cvsignore from input dir. (since testreport no longer run here).
4465 o pkg/thsice:
4466 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
4467 - fix reshaping of sea-ice just after advection:
4468 melt all the ice only if ice-volume is too small.
4469 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
4470 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
4471 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
4472 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
4473 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
4474 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
4475 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
4476 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
4477 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
4478 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
4479 -> update output.txt
4480 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
4481 this affects truncation error: -> update output.txt of exp:
4482 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
4483 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
4484
4485 checkpoint59f (2007/08/21)
4486 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
4487 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
4488 a bounded range (in forward mode)
4489 o pkg/ecco, ctrl, autodiff and mom_common:
4490 internal parameter controls, completements of implementations
4491 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
4492 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
4493 (not seem any difference in testing results).
4494 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
4495 at face corners.
4496 o pkg/generic_advdiff:
4497 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
4498 loop range indices for computing vertical advection tendency
4499 and do the calculation in the interior only (no overlap) ;
4500 for now, only implemented for SOM advection (to save CPU time).
4501 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
4502 o exch2 adjoint
4503 First set of changes:
4504 - add exch2 hand-written adjoint templates
4505 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
4506 This will require cleanup in pkg/autodiff/*.F
4507 (changed routines currently kept separate in verif. code/)
4508 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
4509 that used to hide exch2 or cubed-sphere specific code
4510 (commented via 'cph-exch2')
4511 o pkg/seaice
4512 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
4513 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
4514 output of global_ocean.cs32x15.thsice .
4515
4516 checkpoint59e (2007/07/26)
4517 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
4518 for B-grid vector (not yet tested) and C-grid vector (<- only used
4519 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
4520 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
4521 (#ifdef ALLOW_SALT_PLUME)
4522 o gather_2d/scatter_2d: removed halo regions
4523 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
4524 scheme and the corresponding test case (under front_relax dir). For now,
4525 only available with Skew-flux form and not yet tested in realistic set-up.
4526 adjoint: store directives updated, but gradient checks deteriorated,
4527 so maybe GM/Redi adjoint is now broken.
4528 o seaice adjoint
4529 * add AREA, HEFF, HSNOW as control variable
4530 (should not change lab_sea results)
4531 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
4532 o pkg/seaice:
4533 * added computation of saltFlux in seaice_growth;
4534 For time being, sea ice salinity is assumed constant
4535 contribution of snow flooding to freshening of sea ice is neglected.
4536 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
4537 defaults to 0.0 in order to maintain backward compatibility.
4538 Typical values for SEAICE_salinity are 4 to 10 g/kg.
4539 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
4540 * added SEAICE_availHeatFrac, which specifies fraction of surface level
4541 heat content used to melt or grow ice
4542 * commented out cap of HICE: it helps keep ice thinner
4543 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
4544 * applied OBCS T/S mask to HEFFM sea ice mask
4545
4546 checkpoint59d (2007/06/21)
4547 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
4548 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
4549 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
4550 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
4551 and change default value of parameter "GM_Small_Number";
4552 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
4553 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
4554 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
4555 o pkg/ecco: cost function when applying pkg/smooth to controls
4556 o pkg/ctrl: add forcingPrecond run time parameter
4557 o pkg/seaice:
4558 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
4559 - fix bug in metric terms of u-equation in LSR solver (implicit part),
4560 changes verification/lab_sea
4561 - rearrange implicit part of u-equation in LSR solver to make it easier to
4562 read, understand, and debug. This causes changes at the truncation level.
4563 - fix (serious) bug in the boundary conditions (sign error in the implicit
4564 part) of the LSR solver. Changes all LSR results.
4565 - fixed problem with HSNOW initialization to avoid thick snow when AREA
4566 is initilized with small values - does not change lab_sea results.
4567 - added HsnowFile initialization capability
4568 o pkg/smooth: addition to model/src and pkg/ctrl so allow
4569 initialization of pkg/smooth and application to control vector
4570 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
4571 o dependencies: pkg/profiles requires pkg/cal
4572 o pkg/profiles:
4573 - added option ALLOW_PROFILES_GENERICGRID
4574 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
4575 that interpolation information (grid points and coefficients) is provided
4576 within the netcdf input files.
4577 -> sample matlab scripts can be found in MITgcm_contrib/gael
4578 that allow you to prepare netcdf input files.
4579 - also modified: cleaner include statements, cleaner error print statements,
4580 cleaner stops when error, and more tests of the netcdf input files consistency.
4581 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
4582 o pkg/seaice:
4583 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
4584 requires a new routine: seaice_diagnostics_fill.F
4585 - make sure that seaice does not move if not forced (pressure replacement
4586 method, Hibler and Ip, 1995), changes results
4587 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
4588 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
4589 It is turned off by default (=-1.), because it changes the results.
4590 - make it possible to read AREA from a file, too.
4591
4592 checkpoint59c (2007/06/04)
4593 o add S/R and diagnostics for oceanic mixed-layer depth
4594 o move GMRedi call after all vertical mixing schemes (including KPP)
4595 o pkg/thsice:
4596 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
4597 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
4598 o pkg/obcs:
4599 - bug fix for balance code
4600 o pkg/seaice:
4601 - allow values of SEAICE_elasticParm > 1
4602 - add new parameter SEAICE_evpTauRelax as an alternative
4603 to SEAICE_elasticParm
4604 - make lsr boundary conditions free slip (by default), changes result
4605 - add code for no slip boundary conditions for lsr
4606 - set minimum of zeta to zero (and not 4e8) (changes results)
4607 - add a cap on AREA after advecting AREA if seaice_growth is not called
4608 o change calculation of Visbeck K:
4609 - no longer depend on tapering scheme; instead, compute slope (limited
4610 by GM_maxSlope). this is equivalent to what was comuted before with
4611 clipping or linear tappering.
4612 - fix vertical averaging (wrong by 1/2 level)
4613 - leave the old version (but will not be maintained) within
4614 #ifdef OLD_VISBECK_CALC / #endif
4615 - update output of exp. ideal_2D_oce
4616 o change error catch in calc_r_star to improve vectorization
4617 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
4618 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
4619 o adjoint:
4620 Re-organized adjoint checkpointing according to Matt Mazloff
4621 (but with modifs/completions/cleanups)
4622 Storing is now bundled into large arrays to optimized I/O
4623 (and second step in cleanup of the_main_loop)
4624
4625 checkpoint59b (2007/05/16)
4626 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
4627 - export/import (between ocean & coupler) fields needed for ocean DIC.
4628 o pkg/seaice:
4629 - get rid of three more exchanges seaice_calc_viscosities (required
4630 different loop boundaries in seaice_lsr and seaice_ocean_stress)
4631 - bug fix in seaice_ocean_stress (update of lab_sea required)
4632 - reduce loop boundaries to necessary minimum also in seaice_evp
4633 - go back to the old way of computing deltaC/Z as the adjoint likes that
4634 better
4635 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
4636 passive tracer to an Age Tracer) + update output.txt
4637 o pkg/exf:
4638 - implement A-grid / C-grid selection for wind-stress input files.
4639 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
4640 for now, in exf_bulk_largeyeager04.F only :
4641 - change implementation for case where windspeed + 2. components wind-stress
4642 are read-in. AND use rhoConstFresh to convert evap.
4643 o pkg/seaice:
4644 - use correct EXCH_UV for wind-forcing (on A-grid).
4645 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
4646 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
4647 o pkg/exf:
4648 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
4649 EXF_INTERPOLATION:
4650 - merge global_with_exf/code version of exf_interp_read.F
4651 to the main code ;
4652 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
4653 reading the file ; Important: This options needs to be defined to recover
4654 previous code.
4655 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
4656 - no longer loose real*8 precision along the way when using exf_iprec=64.
4657 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
4658 - change discretisation of evp-solver in order to avoid another exchange
4659 (changes lab_sea) and clean up a little
4660 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
4661 help the adjoint (this also changes the results slightly)
4662 - add a few "_d 0" where they had been missing in seaice_evp.F
4663 - cleaning up: remove unused seaice_calc_rhs.F
4664 o pkg/exf: some cleaning-up:
4665 - change various "constants" into runtime parameters
4666 - cleaned-up Large&Yeager04 routine which should eventually
4667 replace exf_bulkformulae.F (changed names of S/R and CPP)
4668 and merged various ALLOW_ATM_WIND options
4669 only used with thsice pkg (in thsice_get_exf.F):
4670 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
4671 which are used when useStabilityFct_overIce=TRUE (= the default)
4672 - change default values of ice & snow emissivity and scale downward LW
4673 by ice & snow emissivity.
4674 o pkg/thsice:
4675 fix few little problems, in thsice_calc_thickn.F:
4676 - growth vertically (and not laterally) if iceFrac == iceMaskMax
4677 - melt only laterally if hIce < hThinIce (as the comments say)
4678 and in thsice_extend.F:
4679 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
4680 - start to form ice as soon as the minimum ice-volume is reachable.
4681 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
4682 and cpl_aim+ocn
4683 o pkg/kpp
4684 - move computation of surface related input fields to KPP into a new
4685 subroutine kpp_forcing_surf.F
4686 - remove wrong (within bi,bj loops) EXCH calls.
4687 - little cleaning (add argument myThid in last position, cvs header ...)
4688 - for now, fix conservation problem by exchanging KPPviscAz (may not
4689 be the best fix)
4690 o pkg/seaice
4691 - check for inconsistent evp parameter/cpp-flag combination
4692 - remove leftover errIO flat for obsolete name list error handling
4693 o OpenAD
4694 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
4695
4696 checkpoint59a (2007/05/01)
4697 o pkg/seaice: some parameter clarifications and a little bit of clean up
4698 o pkg/thsice: rename run-time parameters:
4699 himin -> hIceMin
4700 himin0 -> hThinIce
4701 hihig -> hThickIce
4702 i0 -> i0swFrac
4703 transCoef -> bMeltCoef
4704 frac_energy -> fracMelting
4705 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
4706 with default values (for now) that do not change the results.
4707 remove old version of thsice vars advection in pkg/seaice.
4708 o in FFIELDS.h:
4709 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
4710 - make pLoad & sIceLoad always available (but still only used if
4711 ATMOSPHERIC_LOADING is #define).
4712 o pkg/kpp: replaced _KPP_RL with _RL
4713 o bug fixes for vertical diffusivity computations when both KPP and
4714 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
4715 are no longer updating the vertical diffusivity array
4716 (passed as argument) but are (re-) setting those arrays.
4717 o pkg/seaice: fix bug in evp solver, while doing that
4718 - change (improve?) discretization of stress computations for both
4719 cgrid-lsr and evp solver
4720 - add a new routine to compute strain rates
4721 - the above changes lab_sea results
4722 - add no slip conditions for evp solver (off by default), lsr-version
4723 may follow
4724 - fix exchange for shear at Z-points (does not change lab_sea)
4725 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
4726 (to force the user to pick a time step since there is not "safe" way
4727 of choosing it)
4728 - add principal stress diagnostics
4729 - rearrange fields for evp a little to avoid having to call a: too many
4730 exchanges and b: exchanges for stress trensor components which we do
4731 not have.
4732 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
4733 of evp, complete rewrite for lsr case (latter is does not yet work
4734 in all cases)
4735 o pkg/kpp: add code to have mixing in shelf ice caverns
4736 - add myThid to all kpp routines (long overdue)
4737
4738 checkpoint59 (2007/04/19)
4739 o pkg/exf:
4740 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
4741 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
4742 - move exf header files from lower_case.h to UPPER_CASE.h ;
4743 add missing cvs Header & Name
4744 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
4745 - add namelist param. selectStressGridPosition, exf_monFreq
4746 - retire many _CLIM routines, and remove data.exf_clim
4747 + params moved to data.exf
4748 + climsst, climsss now handled by exf_set_gen, i.e.
4749 climss?period=0 refers to constant field,
4750 climss?period=-12 to monthly forcing
4751 - split up namelists in data.exf
4752 o pkg/seaice:
4753 - remove seaice_exch and seaice_exch_uv
4754 - remove superfluous exchange of theta
4755 - add myThid to seaice_budget_ocean/ice
4756 - add new interface for atmospheric wind forcing (C-grid only)
4757 + new routine
4758 + two new field (taux, tauy for stress over ice)
4759 + removed one global field (DAIRN) for C-grid case only
4760 o pkg/thsise
4761 - 2nd set of modifs for thsice adjoint in conjunction with exf
4762 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
4763
4764 checkpoint58y_post (2007/04/15)
4765 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
4766 vertical diffusivity, similar to that in MOM4; turned on using
4767 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
4768 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
4769 o Added capability for 3D specification of background vertical diffusion
4770 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
4771 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
4772 "data" file that contains the 3D vertical diffusivity coefficients.
4773 o ice dynamics (pkg/seaice) with thsice thermodynamics:
4774 - add code within pkg thsice to advect & diffuse sea-ice fields
4775 similar to (and will replace) what has been added in seaice_advdiff.F,
4776 but: - conserving Mass, Heat & Salt.
4777 - better when using non-linear advection scheme (not yet fully tested)
4778 - can also be used in atmospheric set-up (for now, only the diffusion).
4779
4780 checkpoint58x_post (2007/04/04)
4781 o IO option for global-file compact format:
4782 - add options when generating topology (utils/exch2/matlab-topology-generator)
4783 - add I/O capability (pkg/mdsio).
4784 - adapt utils/matlab/rdmds.m to read this format.
4785 for now long-line format not yet supported by pkg/mdsio (& exch2).
4786 o shelfice: add a few diagnostics
4787
4788 checkpoint58w_post (2007/03/13)
4789 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
4790 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
4791 (and replace horiVertRatio in NH code).
4792 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
4793 and tutorial_plume_on_slope (sensitive to truncation)
4794 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
4795 directly to drive seaice model (C-grid only)
4796 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
4797 - reintroduce computation of wind from stress,
4798 - compute tau (in exf_bulkformulae.F) from windstress averaged to
4799 mass points to avoid tau = 0
4800 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
4801 o rdmnc.m: make it work with "global" files created with gluemnc
4802 o rdmnc.m : some improvements in dealing with singleton dimension
4803 (tested on all testreport mnc output files).
4804 o genmake2: disable pkg/profiles if netcdf test fails.
4805 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
4806 o move call to cal_readparms up to make calendar parameters/variable available
4807 to all packages
4808
4809 checkpoint58v_post (2007/02/08)
4810 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
4811 useDynP_inEos_Zc tested.
4812 o pkg/exf: changes to properly interpolate/mask/scale initial fields
4813 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
4814 and portions thereof. See read_cs.txt for description and examples.
4815 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
4816 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
4817 following the great-circle arc between those 2 points.
4818 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
4819 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
4820 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
4821 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
4822 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
4823 - still needs work (not working with some options ; efficiency to improve)
4824 and serious testing.
4825 - use this scheme for temperature & salinity in 2 advection test exp.:
4826 advect_xy & advect_xz, respectively.
4827
4828 checkpoint58u_post (2007/01/12)
4829 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
4830 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
4831 o testreport: add option "-skipdir" to skip some test.
4832 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
4833 momentum calculation.
4834 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
4835 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
4836 remove checkpoint.F and the_correction_step.F (no longer used);
4837 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
4838 o add option (linFSConserveTr) to correct for tracer source/sink due to
4839 Linear Free surface
4840 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
4841 o pkg/thsice: fix reading mnc-pickups
4842
4843 checkpoint58t_post (2006/12/30)
4844 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
4845 o pkg/mdsio:
4846 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
4847 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
4848 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
4849 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
4850 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
4851 either MDS_READ_FIELD or MDS_WRITE_FIELD )
4852 - new S/R (to replace MDSWRITEMETA), which allows to write more
4853 informations (variable names, time ...) to meta files.
4854 - modify rdmds.m to give back the meta file content.
4855 o pkg/diagnostics: change vertical interpolation to be safer, and more
4856 flexible (define p-levels to interpolate to in data.diagnostics);
4857 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
4858 diagnostic pointer.
4859 o pkg/seaice: more cleaning up of seaice_growth, added many comments
4860 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
4861 o fix multi-category seaice:
4862 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
4863 SEAICE_MULTICATEGORY
4864 - fix short wave heat flux
4865 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
4866 and allow to use EVP solver. Change forward lab_sea: test both EVP
4867 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
4868 o Initial check-in of lab_sea adjoint
4869 (very similar to natl_box_adjoint/code_seaice)
4870 * used C-grid and EVP solver
4871 * used KPP, GM/Redi
4872 * uses inAdExact=.TRUE.
4873 * gradient checks fail for both ADM and TLM
4874 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
4875 f.d. gradients actually seem more problematic than ADM, TLM gradients;
4876 issue is related to forward mismatch between g77 an ifort
4877 o pkg/seaice: overhaul of thermodynamics
4878 - growth.F and groatb.F are replaced by new routine seaice_growth.F
4879 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
4880 - move a few global fields out of SEAICE.h into seaice_growth.F and
4881 make them 2D (FICE/QNETO/ ...)
4882 - remove FO (it is the same as QNETO)
4883 - introduce a few local fields to avoid modifying external fields such
4884 as atemp, etc.
4885
4886 checkpoint58s_post (2006/12/11)
4887 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
4888 changed exf_set_gen.F so that
4889 genperiod=0 means input file is one time-constant field and
4890 genperiod=-12 means input file contains 12 monthly means
4891 o CG2D: use pre-computed solver main-diagonal (stored in common block);
4892 this affects truncation error ; generate new output file for exp. which
4893 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
4894 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
4895 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
4896 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
4897 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
4898 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
4899 o start implementation of deep-atmosphere and anelastic formulation
4900 o verification: remove 2nd copy of input files and use script "prepare_run"
4901 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
4902 o mom_common/vecinv/fluxform: fix a few initialisation isssues
4903 o profiles: fix for multithreaded case
4904
4905 o diagnostics: rename few diags:
4906 s/'PRESSURE'/'RCENTER '/g
4907 s/'TICE '/'oceFreez'/g
4908 s/'TAUX '/'oceTAUX '/g
4909 s/'TAUY '/'oceTAUY '/g
4910 s/'SWFLUX '/'oceQsw '/g
4911 s/DIFx/DFxE/g
4912 s/DIFy/DFyE/g
4913 and add few ocean-forcing diagnostics:
4914 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
4915 o modifications to pkg/seaice/growth.F and budget.F, which change results of
4916 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
4917 as actual snow thickness. It now refers everywhere to effective snow
4918 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
4919
4920 checkpoint58r_post (2006/11/17)
4921 o modifications to pkg/seaice/growth.F, which change results of
4922 lab_sea experiment: fixes pertain to melting snow over open water, to
4923 masking EVAP under sea ice, and to using the correct AREA variable for
4924 computations of EVAP, PRECIP, HSNOW, and GHEFF
4925 o add ability to read bathy, salt, and theta using MNC (off by def)
4926 o add flooding algorithm and advection of HSNOW for pkg/seaice;
4927 both are turned off by default and do no change any results
4928 o seaice advection with pkg/thsice: a step toward the use of non-linear
4929 advection scheme, but #ifdef or commented out for now (requires more EXCH).
4930 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
4931 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
4932 in natl_box (affects results @ truncation level: update output.txt)
4933 o multi-threading and IO:
4934 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
4935 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
4936 (needed to work with SingleCpuIO): tested in all verif. exp.
4937 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
4938 affects the results (but none of the verification test uses this scheme).
4939 o Adding some pkg/diagnostics capability to pkg/seaice
4940 (will certainly be subject to changes)
4941 o ctrl: adding new control variables:
4942 lwflux, lwdown, evap, snowprecip, apressure, runoff
4943
4944 checkpoint58q_post (2006/10/20)
4945 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
4946 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
4947 high_res_cube configuration by 4% on Columbia.
4948 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
4949 add (in global_with_exf/code) a version of EXF_INTERP_READ without
4950 dynamical allocation (seems to work in multi-threaded).
4951 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
4952 single CPU io) so that TAF does not have to see EESUPPORT.h
4953 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
4954
4955 checkpoint58p_post (2006/09/08)
4956 o obcs: stop if obcs is used with useCDscheme = .true.
4957 o shelfice:
4958 - fix a sign error so that no slip at shelfice interface works
4959 - remove stop for combination non-hydrostatic code and shelfice. That does
4960 not mean, that the results are correct, but at least they are numerically
4961 stable
4962 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
4963 o added adjoint exch routined for all exch*3d* routines
4964 and updated flow directives
4965
4966 checkpoint58o_post (2006/08/28)
4967 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
4968 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
4969 o change controling S/R for writing pickup file (new S/R do_write_pickup)
4970 and clean-up reading/writing of pickup files.
4971 o fix local version of read/write pickup (NH part) in rotating_tank/code
4972 o simplify EXCH interface:
4973 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
4974 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
4975 o added the regrid package
4976 o shelfice:
4977 - add a simple boundary layer scheme to reduce noise
4978 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
4979
4980 checkpoint58n_post (2006/08/14)
4981 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
4982 local variable (not in common block).
4983 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
4984 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
4985 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
4986 to work with SingleCpuIO.
4987 o add "_d 0" to real constant of pkg/cfc subroutines ;
4988 update exp. cfc_exemple & tutorial_cfc_offline output files.
4989 o multi-threading and IO:
4990 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
4991 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
4992 - barrier before and after reading.
4993 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
4994 - avoid using MDS_WRITELOCAL for LAND pkg output.
4995 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
4996 common-block variables ; Allows multi-threading with master-thread IO.
4997 o change default MAX_NO_THREADS from 32 to 4 ;
4998 and stop cleanly when MAX_NO_THREADS is too small.
4999 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
5000
5001 checkpoint58m_post (2006/07/17)
5002 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
5003 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
5004 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
5005 keep global_ocean.90x40x15 (for AD testing) with former secondary test
5006 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
5007 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
5008 add MITgcm_tutorials (= code + all the tutorials)
5009 o ecco, option to compute cost for total ssh (mean+anom)
5010 o consistent with addition of ptracer and ssh in pkg/profiles
5011 o profiles: adding ptracer and ssh
5012 o testreport: change multi-test output-file name
5013 (from output.txt.{name} to output.{name}.txt)
5014 o profiles: now ok for mutli-tiles case
5015 o seaice: add 4 parameters for different advection schemes for area,
5016 (effective) seaice thickness, enthalphy, and snow height. Their default
5017 is the standard parameter SEAICEadvScheme
5018 o calc_gw:
5019 - add cosFacU in zonal viscous flux (harmonic.visc.).
5020 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
5021 of tutorial_plume_on_slope.
5022 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
5023 o calc_gw: true flux-form, account for horizontal grid spacing.
5024 update rotating_tank results, but not plume_on_slope (affected at
5025 truncation level, 11 digits).
5026
5027 checkpoint58l_post (2006/07/12)
5028 o calc_gw:
5029 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
5030 - remove side-drag for now (need to fix it); update plume_on_slope results.
5031 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
5032 o commit code to make SST/SSS weights spatially variable
5033 (based on either variable in-situ or variable initial T/S weights)
5034 o pkg/ecco:
5035 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
5036 now based on horizontally varying weights wthetaLev, wsaltLev
5037 * cost_averagesflags now returns year indices in addition to day, month
5038 * sflux balance is performed on annual basis
5039 (sflxumm, sfluxmm2, bal_sfluxmm)
5040 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
5041 including separate counting and multipliers
5042 o pkg/rbcs
5043 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
5044
5045 checkpoint58k_post (2006/07/06)
5046 o testreport:
5047 - always build in dir. "build" (if not there, mkdir build instead of building
5048 & running in input)
5049 - run in dir run (if it exists), in build otherwise.
5050 - call prepare_run (if input/prepare_run exists)
5051 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
5052 o pkg/exf modifications to interpolation and rotation routines for more
5053 reasonable treatment of North Pole singularity: for tracers North Pole
5054 value is set to northernmost zonal-mean value, for zonal velocity it is
5055 set to zero, and for meridional velocity it is set to northernmost value.
5056 o pkg/exf/exf_check_range.F
5057 - add tile index to diagnostics and move stop statement to the very
5058 end of the routine.
5059 o pkg/diagnostics: (diagnostics_main_init.F)
5060 define title of isomorphic variables according to the current config.
5061 o pkg/thsice with pkg/seaice dynamics:
5062 - fix domain of computation (interior only, required for exf) and do exchanges
5063 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
5064 o towards a standard way of dealing with multi-threading in MONITOR
5065 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
5066 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
5067 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
5068 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
5069 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
5070 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
5071 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
5072 o tracer advection:
5073 - clean-up and simplify calc_common_factors.F
5074 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
5075 advection subroutine (but still not used within DST advection S/R)
5076 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
5077
5078 checkpoint58j_post (2006/06/15)
5079 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
5080 from file (collects calls previously in FORWARD_STEP)
5081 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
5082 o adjoint store dir. adjusted accordingly
5083 o genmake2
5084 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
5085
5086 checkpoint58i_post (2006/06/14)
5087 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
5088 on wind stress (SEAICEstressFactor defaults to 1.)
5089 o Total number of Timers is finite (<=40): comment out 2 non-essential one
5090 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
5091 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
5092 on CS-grid: no longer loosing mass.
5093 o exf & curvilinear-grid: no longer modify longitude xC & xG.
5094 o pkg/ggl90: fix sloppy output and fix a bug
5095 o pkg/seaice: added SEAICEuseEVPpickup parameter
5096 - Set to false in order to start EVP solver with
5097 non-EVP pickup files when using SEAICEuseEVP
5098 - fix sign error in diffusion in seaice_calc_rhs
5099
5100 checkpoint58h_post (2006/06/07)
5101 * Modifications for bottom topography control
5102 o replace hFacC by _hFacC at various places
5103 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
5104 o add non-self-adjoint cg2d_nsa
5105 o update autodiff support routines
5106 o re-initialise hfac after ctrl_depth_ini
5107 o works for 5x5 box, doesnt work for global_ocean.90x40x15
5108 * Adding verification for 5x5 box (4-layer) bottom topography control
5109
5110 checkpoint58g_post (2006/06/07)
5111 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
5112 used for mean seasonal cycle, mean diurnal cycle); add an example
5113 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
5114 o pkg/ggl90:
5115 - add parameter (minimum surface kinetic energy)
5116 - fix bug (avoiding division by zero)
5117 o couple pkg/thsice to pkg/seaice:
5118 - modify advection in seaice to accomodate new scalar fields to be advected
5119 - only muliDimAdection scheme work with seaice/thsice
5120 - mapping of thsice-variables to seaice-variables, back and forth
5121 - does not break the verification experiments, but does not give the
5122 desired results either
5123 o pkg/seaice
5124 - make (default) second order advection a bit less confusing?
5125
5126 checkpoint58f_post (2006/06/05)
5127 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
5128 to pkg/seaice):
5129 - new routines thsice_map_exf and thsice_get_exf provide the interface
5130 - add an additional formal parameter to thsice_solve4temp
5131 o pkg/exf:
5132 - add new fields wspeed, snowprecip (to be able to couple to thsice)
5133 - correct Stefan-Boltzmann constant
5134 - new parameter for longwave surface emittance
5135 - separate some stuff from exf_bulkformulae into new routines
5136 exf_radiation, exf_wind
5137 - add new parameters and constants: longwave emissivity for ocean, ice
5138 and snow, evaporation parameters over ice
5139 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
5140 either wind from stress or stress from wind
5141 o pkg/thSIce:
5142 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
5143 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
5144 and THSICE_CALC_THICKN
5145 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
5146 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
5147 to make debugging easier.
5148 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
5149 o pkg/bulk_force:
5150 - clean-up comments and parameters ;
5151 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
5152 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
5153 generate new output for test-experiment: aim.5l_cs.thSI
5154 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
5155 testreport accordingly
5156
5157 checkpoint58e_post (2006/05/17)
5158 o SEAICE_CGRID adjoint done
5159 o R_STAR adjoint implemented.
5160 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
5161 * need to sort out init. of h0facc, etc.
5162 o Make pkg/profile fully independent of ecco,cost, etc. stuff
5163 to be able to use it in pure forward.
5164
5165 checkpoint58d_post (2006/04/21)
5166 o upgrade simple test-experiment to tutorial example:
5167 step.1: duplicate the experiment and (step.2) will remove the old copy.
5168 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
5169 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
5170 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
5171 tutorial_global_oce_biogeo <- copy of dic_example
5172 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
5173 tutorial_plume_on_slope <- copy of plume_on_slope
5174 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
5175 tutorial_global_oce_optim <- empty for now (David ?)
5176 tutorial_global_oce_in_p <- copy of global_ocean_pressure
5177 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
5178 o correct a sign problem in cost_scat.F
5179 o obcs and ptracers: fix boundary conditions for advections schemes
5180 with larger stencil
5181 o thsice adjoint: start
5182 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
5183 completeness
5184 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
5185 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
5186 o ptracers adjoint:
5187 * avoid extensive recomputatations
5188 * fix missing re-init. of gptr (missed by TAF)
5189 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
5190 me to turn off the excessive output to STDOUT that this package produces
5191 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
5192 and add those terms in Vector-Invariant formulation.
5193 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
5194 if the control period (xx_hfluxperiod etc) is 0
5195 o in profiles pkg, clean routines and fix details
5196 o in ecco pkg, reading ssh data:
5197 fix problem in case the model does not start at iter0=0
5198 o fix mnc-pickup/restart for ptracers
5199 o new package prifiles:
5200 code to compute profile-based cost by Gael Forget
5201 (modifs in ecco, ctrl, autodiff)
5202 o Benign bug fix in initialization (spotted by M. Mazloff) of
5203 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
5204
5205 checkpoint58c_post (2006/03/23)
5206 o adjoint: finish NLFS adjoint and provide reference output in
5207 verification/global_ocean.90x40x15/results_ad_nlfs
5208 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
5209 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
5210 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
5211 with SEAICE_CGRID defined.
5212 o move calendarDumps from "data" to "data.cal" and clean-up the code
5213 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
5214 o add useEXF & useCAL flags (for now, set in hard-coded way)
5215 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
5216 (were missing in NH mode, and wrong in quasihydrostatic mode).
5217 waiting for Chris updated version of calc_gw to add those CALLs.
5218 o fix bug in quasihydrostatic S/R ;
5219 add a test for this option: global_ocean.90x40x15.qshyd
5220 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
5221 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
5222 o add on/off flag useOffLine for package OFFLINE
5223 o seaice:
5224 - modify advection so that it works also on the C-grid
5225 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
5226 problem in multi-tile runs with C-grid
5227 - add flags for clipping ice velocities and/or masking solver forcing
5228 - fix drag (ocean on ice) formulation and a bug that caused noise in the
5229 C-grid solver
5230 - added a few comments to seaice_diffusion.F
5231 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
5232 are now exclusive)
5233 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
5234 required re-ordering the code a little:
5235 + make DAIRN global variable (defined in SEAICE)
5236 + move computation of the viscosities eta and zeta into a new separate
5237 routine (because I need to recompute them in seaice_ocean_stress.F)
5238
5239 checkpoint58b_post (2006/03/13)
5240 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
5241 update output.txt of exp. aim.5l_cs.thSI
5242 o various mnc cleanups and improvements:
5243 + shrink lookup tables by factor of ~4
5244 + better error reporting when running out of lookup space
5245 + able to handle longer path/file names (up to 500 chars)
5246 o adjoint:
5247 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
5248 - TBD: "hidden" mom_vecinv recomp. in dynamics
5249 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
5250 (allow to differentiate between forcing components using new integer flags:
5251 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
5252 and add new flag to put Dissipation tendency out of Adams-Bashforth.
5253 o ecco
5254 - enable trend removal from SSH anomaly obs.
5255 o adjoint
5256 - a fix for PmEpR when #undef EXACT_CONSERV
5257 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
5258 - try to fix "hidden" recomp. in forward_step for NLFS
5259 (NLFS seems broken sometimes after I checked it in)
5260 o seaice:
5261 - add c-grid version of the dynamic solver:
5262 + three new routines that are the c-grid substitute lsr, dynsolver
5263 and ostres
5264 + put a few fields that were local to dynsolver into global common
5265 blocks, so that I can move the computation of stresses etc into
5266 seaice_lsr (saves coding but may break the adjoint).
5267 - replace more hardwired parameters by runtime parameters
5268 - add ice masks that mask the rhs of the implicit solvers where there
5269 is no ice (commented out in seaice_dynsolver, because i am not sure
5270 if this works properly), eventually this should replace the clipping
5271 of ice velocities in seaice_dynsolver to +/-40cm/s.
5272 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
5273 include it only where its needed
5274 o move balancing of fluxes before the call of external_forcing_surf
5275 o seaice:
5276 - correct units of turning angles (now they are really in degrees)
5277 - move computation of GWATX/Y out of main routine into dynsolver
5278 - initialize GWATX/Y in seaice_init
5279 o Apply mask on Fresh-Water flux (needed for SSH forcing).
5280 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
5281 o seaice: add runtime flags for turning angles (default to zero)
5282 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
5283 and trend from exf forcing and ctrl control adjustments
5284 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
5285 (since checkpoint57x_post)
5286 o change the default rotation period to 86164.s = the Earth rotation
5287 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
5288 and based on a reference stratification. Tested within hs94.cs-32x32x5.
5289 o seaice advection: add code for choosing between the default (2nd order
5290 central differences) and multiDim advection schemes provided by
5291 pkg/generic_advdiff
5292 o seaice:
5293 - removed all references to SEAICE_GRID.h fields from
5294 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
5295 (cubed-sphere configuration will change a little)
5296 - grid computations in seaice_init are obsolete now.
5297 - cleaned up code a little so that is easier to read (hopefully).
5298 - added new (better?) discretizations of default advection and diffusion
5299 (turn on with SEAICEuseFluxForm)
5300 - replace 1 in 3d global fields by kSurface in growth.F
5301
5302 checkpoint58a_post (2006/02/13)
5303 o seaice:
5304 - bug fix in advect.F
5305 o shelfice:
5306 - separate shelfice load anomaly from pload (breaks with time
5307 dependent forcing), => introduce constant field shelficeLoadAnomaly.
5308 Its default is 0., but it may be computed more cleverly from (unknown)
5309 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
5310 done offline. A good approximation of the pressure load anomaly is
5311 necessary to avoid large initial adjustment processes underneath
5312 deep-reaching shelfice.
5313 - small fix in ISOMIP shelfice_thermodynamics
5314 - add more sophisticated thermodynamics of Hellmer (1989), this is
5315 now the default
5316 - give a few constants more intuitive names
5317 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
5318 if bulk formulae are used in long integration (especially EmPmR). Turn
5319 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
5320 if balancePrintMean, the imbalance that is substracted is printed to
5321 STDOUT.
5322 o fix bug (typo) in obcs_apply_eta.F
5323 o add a new package shelfice which enables us to model the circulation
5324 underneath shelf-ice with draughts of hundreds of meters.
5325 - works
5326 - to do: + include improved thermodynamics
5327 + check whether kSurfC (from model/inc/SURFACE.h) can be used
5328 instead of new field kTopC
5329 + can we use topoFile, Ro_surf and existing code in ini_depth.F
5330 instead of new field R_shelfIce and new code in ini_depth.F
5331 and ini_mask_etc.F?
5332 + adjust vertical mixing schemes?
5333 o seaice pkg:
5334 - add a cpp-flag to include a simple formula for a salinity dependent
5335 freezing point of sea water at the surface
5336 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
5337 meridional stresses are now different (and hopefully correct)
5338 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
5339 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
5340 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
5341 o pkg/diagnostics: add options and parameters for regional-statistics
5342 diagnostics ; define regions by reading a region-mask from a file
5343 (might add other options later)
5344 o pkg/bulk_force:
5345 - add option and parameters to use AIM surface-flux formulae.
5346 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
5347 others forcing fields (defined in PARM05, parameter file "data") are loaded
5348 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
5349 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
5350 - use the right EXCH call for uwind,vwind (to work on CS-grid).
5351 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
5352 and parameters (note: calcWindStress replaces .NOT.readwindstress).
5353 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
5354
5355 checkpoint58 (2006/01/12)
5356 o add "--embed-source" option to genmake2 which, when the supporting
5357 tools can be compiled (as determined by genmake2) will turn on the
5358 embed_files package which then embeds the entire MITgcm source code
5359 (*.[fFhc] + Makefile) used for the build within the executable
5360 - requested by CNH but off by default
5361 - adds a paltry <9MB to the mitgcmuv executable in most cases
5362 - only writes the output when useEMBEDSRC in eedata is true
5363 o clean up 3-dim. relaxation codes:
5364 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
5365 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
5366 * Thanks to Tom Haine for testing!
5367
5368 checkpoint57z_post (2005/12/31)
5369 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
5370 affects output (@ truncation level) of exp. plume_on_slope ; updated.
5371 o fix the pickup behavior for obcs in combination with ptracers
5372 o fix a bug in ptracers_external_fields_load
5373 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
5374 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
5375 o transfered surface NH pressure to eta field (if exactConserv).
5376 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
5377 and update lab_sea output.txt file.
5378 o completing 3-dim. relaxation code: additional term
5379 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
5380 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
5381 * At compile time, in "EXF_OPTIONS.h" set
5382 #define ALLOW_CLIMTEMP_RELAXATION
5383 #define ALLOW_CLIMSALT_RELAXATION
5384 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
5385 tauThetaClimRelax3Dim = 15552000.0,
5386 tauSaltClimRelax3Dim = 15552000.0,
5387 * 3 cases:
5388 1) Use a constant-in-time 3-dim. field
5389 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
5390 3) Real-time relax. to time-evolving prescribed field
5391 o Adding Laplacian-type smoothness constraint on
5392 initial and boundary (forcing) controls (ic, bc)
5393 * enable at compile-time via
5394 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
5395 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
5396 * Absolute scale somewhat unclear so far
5397 * no area weighting was included since no other cost term does so far
5398
5399 checkpoint57y_post (2005/12/08)
5400 First step for a NLFS adjoint
5401 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
5402 o new init. routines for calc_r_star, calc_surf_dr
5403 o still need to deal with ini_masks_etc
5404 o testreport seemed happy
5405 checkpoint57y_pre (2005/12/08)
5406
5407 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
5408 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
5409 o add new offset feature to offline pkg (plus minor cleanup)
5410 o cfc fixes for final year of integration
5411 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
5412 be in GCHEM_OPTIONS).
5413
5414 checkpoint57x_post (2005/12/04)
5415 o fix testreport Pb in multiple test experiment.
5416 o cleanup our namelist syntax in verification:
5417 - make it more F95 standards compliant (some work still needed)
5418 - allows the vast majority of our tests to work with gfortran
5419 o Non-Hydrostatic:
5420 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
5421 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
5422 o Allow to apply AB on T,S rather than on AB(gT,gS):
5423 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
5424 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
5425 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
5426 - need a "clever" read_pickup to restart from the other AB formulation
5427 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
5428 o remove some unused variables (reduces number of compiler warnings)
5429 o adjoint
5430 * Disable useVariableViscosity for adjoint for time being
5431 (there are a number of extensive recomputations)
5432 * Initialize certain variables needed for adjoint
5433
5434 checkpoint57w_post (2005/11/03)
5435 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
5436 fix the singleCpuIO RS version of MDSWRITEFIELD
5437 and add a WARNING if using globalFiles=T with multi-processors.
5438 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
5439 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
5440 o tracer advection scheme:
5441 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
5442 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
5443 was not very convenient).
5444 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
5445 (further tests needed for the implicit DST & Flux-Limiter schemes).
5446 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
5447 and sRef for convenience, handy, when you want to initialize
5448 ptracers in a large domain with a constant non-zero value. Also,
5449 untangle ptracers_init.F a little.
5450
5451 checkpoint57v_post (2005/10/13)
5452 o change dome exp. to use variable viscosity in side-drag terms.
5453 o remove all the files from the cfc_offline test since they are now
5454 incorporated into tutorial_cfc_offline which has been producing
5455 identical results for a few days of testing
5456 o add new parameter: sideDragFactor to enable half-slip-side BC
5457 and change side-drag S/R to use viscosity from mom_calc_visc
5458 (can switch back by setting sideDragFactor=0.); affects results at
5459 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
5460 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
5461 o vorticity & strain are now computed without masking, to account for
5462 no-slip-side BC in variable viscosity calculation ; mask is applied
5463 anyway later on, before computing advection/coriolis terms.
5464 o modify exp4 to test new obcs support for reading from external files
5465 and for passive tracers
5466 o fix behavior of ptracers_monitor when monitor output is written to a
5467 netcdf-file; still not independent of monitor.F (writes in the same
5468 file).
5469 o change default value of tRef (put a uniform, meaningful value for ocean
5470 & atmos) and initialize sRef (was missing, as Martin mentioned).
5471 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
5472 to be proportional to enstrophy dissipation length. Thus,
5473 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
5474 This is now consistent with Smagorinsky and with the manual.
5475
5476 checkpoint57u_post
5477 o OBCS and PTRACERS: add open boundary support for passive tracers
5478 - either use homogenous (pseudo) v.Neumann conditions or prescribe
5479 OB-values from file; this is not different from the way theta and salinity
5480 are treated
5481 - however, Orlanski-radiation conditions are not supported, and the model
5482 will stop if you use pTracers and Orlanski at the same time.
5483 - beefed up the rountine obcs_external_fields_load: now only those open
5484 boundary values are overwritten with values from files for which there
5485 are really files, otherwise the OB-fields remain untouched. This makes
5486 it possible to use different OBs at different ends of the domain (as
5487 with EXF)
5488 o reduce number of exch calls in shap_filt (s2).
5489 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
5490 truncation level) 4/5 MLAdjust test results (11&12 digits match).
5491
5492 checkpoint57t_post (2005/10/03)
5493 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
5494 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
5495 same truncation, independent of the face number: affects affects several
5496 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
5497 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
5498 note that biharmonic viscosity + no-slip was not tested in any experiment.
5499 o fix bug in non-linear free-surf side-drag ; generate new output for
5500 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
5501 o make mnc honor the writeBinaryPrec flag for most kinds of output
5502 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
5503 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
5504 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
5505 o add brackets in multi-terms sum to get same truncation, independent of
5506 the face number (manage to get exactly same value of gU,gV at the cs-edge)
5507 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
5508 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
5509 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
5510 a maximum grid-scale Reynolds number. Also, changes all length calculations
5511 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
5512 Suggested values of viscosity parameters found in mom_calc_visc.
5513 Many new viscosity diagnostics available.
5514
5515 checkpoint57s_post (2005/09/20)
5516 o Add clearing-house for viscosity calculations, mom_calc_visc and
5517 correct numerous bugs in LeithD and Smagorinsky discretizations.
5518 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
5519 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
5520 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
5521 and with Strain-Tension viscous term calculation (mom_hdissip.F).
5522 The Strain-Tension form is now called with useStrainTensonVisc=.true.
5523 ViscAhStrain and viscAhTension are now retired.
5524 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
5525 o In response to JMC's bug report, genmake2 now ignores any soft-links
5526 that it finds in the *current* directory when searching for files.
5527 Soft-links found in any other source directories will still work as
5528 they did before.
5529 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
5530 a C routine to unlimit the stack size
5531 o mnc-ify pkg/aim snapshot vars
5532 o mnc-ify pkg/land as requested by Daniel
5533 o various changes to mnc including:
5534 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
5535 - output can now be grouped so that all files within a group
5536 change the ITER portion of their names in lock-step together
5537 - can now read ("global") PER-FACE (in addition to PER-TILE) files
5538 and works with both EXCH1 and EXCH2 (but needs more testing)
5539 - writing works for all verification test cases w/ g77 on Linux
5540
5541 checkpoint57r_post (2005/09/07)
5542 o make MNC variable initialization happen earlier
5543 o add diagnostics for (almost) each term of the momentum Eq.
5544 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
5545 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
5546 o remove MINIMAL_TAVE_OUTPUT option ;
5547 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
5548 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
5549 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5550 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
5551 o add time-dependent SST, SSS control
5552 o cost terms in ecco/ modularized (new cost_generic.F)
5553 o cost_averages routines are modularized (new cost_averagesgeneric.F)
5554 o new infrastructure for seaice model vs. obs misfits in seaice/
5555 * driver from the_main_loop.F is seaice_cost_driver.F
5556 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
5557 * gradient check in Exp. 6a of natl_box_adjoint/
5558 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
5559 (see README file)
5560
5561 checkpoint57q_post (2005/08/19)
5562 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
5563 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
5564 - bug was reported by Jean-Michel and Ian Fenty
5565 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
5566 update exp. cpl_aim+ocn output.
5567 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
5568 Needed for high-res. runs with large global files
5569 to be able to limit tapelev size
5570 o Changed some tests for adjoint:
5571 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
5572 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
5573 * global_ocean.90x40x15/ back to default 3-level checkpointing
5574 o Modifications to enable scripted COMMON to MODULE conversion
5575 * verification/OpenAD/code/ has necessary scripts and description;
5576 * converts, compiles and runs successfully;
5577
5578 checkpoint57p_post (2005/08/01)
5579 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
5580 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
5581 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
5582 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
5583 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
5584 (was already the case for dissipation with mom_vecinv,
5585 and also the case for grad.PhiHyd when staggered-timeStep)
5586 This will allow to put dissipation out-off the AB time-stepping.
5587 Unfortunately, affects truncation error. Update output of exp. that "fails"
5588 (cg2d matching number) and leave the others for later: front_relax(10),
5589 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
5590 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
5591
5592 checkpoint57o_post (2005/07/30)
5593 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
5594 (2) its ready to be documented during the 20050801 DocFest
5595 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
5596 for ideal_2D_oce and lab_sea on linux_ia32_g77
5597 o set to #undef CTRL_SET_OLD_MAXCVARS_30
5598 in global1x1_tot/code_seaice_adj to access indices 32, 33
5599 (worth another tag)
5600
5601 checkpoint57n_post (2005/07/29)
5602 o adding precip control xx_precip 32
5603 o adding swflux control xx_swflux 33
5604 o Replacing 10 forcing penalty cost routines by 1 generic.
5605 o Implementing partitioning in time-mean and variable adjustment
5606 for atmos. state.
5607 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
5608 o in natl_box_adjoint:
5609 * updated exp 1 to 10
5610 (but does not have time-mean vs. variable split results yet)
5611 o updated global1x1/*_seaice_adj/
5612 to incorporate latest changes
5613 o enable useSingleCpuIO for mdsio vector routines
5614 (applies in particular to tapelev I/O)
5615 o removed inefficient K-loop in all active_file*control*.F
5616
5617 checkpoint57m_post (2005/07/28)
5618 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
5619 and advect_cs (use EXCH-2 and standard cs-32 grid files).
5620 o pkg/exch2: filling of face-corner halo regions is optional
5621 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
5622
5623 checkpoint57l_post (2005/07/14)
5624 tag before updating tutorials (pre-release-2)
5625 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
5626 for output and interpolation of input fields onto model grid)
5627 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
5628 Affects results of exp. rotating_tank ; update output.txt.
5629 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
5630 and taking the square quantity and/or using a fraction-weight field.
5631 o fix aim_diagnostics_init.F mate numbers.
5632 o add mnc output capability to diagnostics/diagstat and update
5633 our cvsignore files for the ACSII output generated
5634
5635 checkpoint57k_post (2005/07/02)
5636 o lab_sea now uses diagnostics package and provides a suite of
5637 new EXF diagnostics output.
5638
5639 checkpoint57j_post (2005/06/30)
5640 o exf
5641 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
5642 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
5643 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
5644 * extended diagnostics output
5645 - now includes all EXF variables
5646 - hs, hl moved to common block
5647 - separate S/R for diagnostics, called after ctrl vector is added
5648 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
5649 - EXFqnet contains true Qnet (i.e. includes qsw)
5650 * updated verif. lab_sea, global_with_exf
5651 * Rearranging hflux (exf_mapfields -> exf_getforcing)
5652 to ensure that diagnostics sees a true EXFqnet
5653 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
5654 o diagnostics pkg: change pointers so that 1 diagnostic can be used
5655 several times with different frequencies.
5656 o mnc-ify the thsice package as requested by Daniel Enderton
5657 - the monitor--MNC output needs work
5658 - many attributes need to be added (most are currently blank)
5659 o mnc-ify theaim_v23 package as requested by Daniel Enderton
5660 - many attributes need to be added (most are currently blank)
5661 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
5662 o add Sadourny like discretization to the 4th.O vorticity advection scheme
5663 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
5664 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
5665 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
5666 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
5667 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
5668
5669 checkpoint57i_post (2005/06/19)
5670 o Diagnostics package was changed: diagnostic allocation is now deactivated
5671 by setting an empty file name in the namelist (used to be by setting 0 frequency)
5672 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
5673 add 1rst Order upwind vertical Shear.
5674 o add a quick fix for A/B checkpointing in OFFLINE mode
5675 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
5676 end-run around the C/Fortran linking horror in eesup/src/timers.F
5677 o added pkg/runclock: allows user to terminate run based on wall clock
5678 o added non-hydrostatic scaling parameter: nh_am2
5679 o pkg/my82: futile attempt to make results compiler-independent by adding
5680 some "_d 0", etc. no effect.
5681 o for mnc output, fill the 'T' coordinate var with myTime and create a
5682 separate 'iter' variable for iteration count
5683 o pkg/diagnostics:
5684 add new capability: output of Global/Regional & per-level statistics ;
5685 tested against monitor output (including land & thSIce) on various exp.
5686 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
5687
5688 checkpoint57h_done (2005/05/19)
5689 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
5690 data.diagnostics, data.gchem, data.ptracers) is done.
5691
5692 o pkg/diagnostics: prepare for Global/Regional statistics.
5693 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
5694 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
5695 and rename it: DIFFERENT_MULTIPLE
5696
5697 checkpoint57h_post (2005/05/14)
5698 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
5699 o pkg/diagnostics: change output frequency, now in seconds (instead
5700 of Nb of iterations). This requires to change data.diagnostics.
5701 checkpoint57h_pre (2005/05/12)
5702
5703 o in mnc, let the user create the output dir if both mnc_outdir_date
5704 and mnc_outdir_num are false
5705 o add fflags() to pkg/diagnostics which allows one to specify, on a
5706 per-file basis, the file precision [default behavior is unchanged]
5707 o added diagnostics to pkg/kpp, including computation of mixed layer
5708 depth based on a temperature/density criterion
5709 o updated verification/natl_box to test the new pkg/kpp diagnostics
5710 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
5711 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
5712 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
5713 not mnc -- this mistake was found by JMC and is now corrected
5714
5715 checkpoint57g_post (2005/04/15)
5716 o add Adams-Bashforth 3rd Order time stepping:
5717 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
5718 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
5719 checkpoint57g_pre (2005/04/15)
5720
5721 o make lambda[Theta,Salt]ClimRelax spatially varying
5722 (default remains spatially uniform constant based on tau)
5723 o added new control variables
5724 * init. uVel, vVel, etanN
5725 * lambda[Theta,Salt]ClimRelax
5726 o separate masks used for ctrl_pack/unpack 'from write_grid' output
5727 (suggested by G. Forget)
5728
5729 checkpoint57f_post (2005/04/06)
5730 o add parameter "baseTime" = model base time = time at iteration zero
5731 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
5732 account for baseTime shift
5733 o move Coriolis arrays from PARAMS.h to GRID.h
5734 checkpoint57f_pre (2005/04/06)
5735
5736 o mnc-ifying the seaice package
5737 o introduced an alternative length scale calculation for use in the limiting
5738 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
5739 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
5740 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
5741 as well as grad(vort3). Made it compatible with both approximate form
5742 for the cubed sphere and full form of these gradients. Added flag
5743 useFullLeith to select between approximate and full form.
5744 o add "d0" in getcon.F to reduce differences between compilers/platforms
5745 update output.txt of exp. fizhi-gridalt-hs
5746 o change port_rand funtion to allow to set the seed.
5747 o fix obscure MNC bug involving conversion between reals and integers
5748 - it caused no problems with certain (eg. gcc, ifc) compilers but the
5749 new version is now more standards-compliant
5750 o adjoint-related modifications
5751 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
5752 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
5753 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
5754
5755 checkpoint57e_post (2005/02/28)
5756 o Adding eddy stress controls a la Ferreira et al.
5757 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
5758
5759 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
5760 update output.txt of exp. fizhi-gridalt-hs
5761 o add more "Z" dimensions and associated coordinate vars to MNC
5762 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
5763 o parameter calendarDumps: when set, approximate months (30-31 days) and years
5764 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
5765 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
5766 months and years. Requires pkg/cal.
5767 o diagnostics: add pickup functionality
5768 - off by default for backwards compatibility
5769 - current version only uses MDSIO -- MNC will be added
5770 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
5771 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
5772
5773 checkpoint57d_post (2005/02/11)
5774 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
5775 o modify verification/ideal_2D_oce so that it tests the creation of mnc
5776 output from the diagnostics package
5777 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
5778 o make genmake2 more portable by using ".$FS" instead of ".f" for more
5779 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
5780 o add coordinate variables to the MNC output from the diagnostics package
5781 o change MNC-flags default value: true when useMNC=TRUE
5782 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
5783 the ability (off by default) to read the grid information using MNC
5784 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
5785 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
5786 o do snap-shot diagnostics at the middle of the time-interval (instead of
5787 at the end).
5788 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
5789 new test for AIM with thSIce + slab-ocean
5790 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
5791 o move state variable diagnostics to the beginning of the time step ;
5792 (note: still needs some work specially for snap-shot diagnostics)
5793 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
5794
5795 checkpoint57c_post (2005/01/27)
5796 o Change testing option (-ieee) to get closer agreement between g77 & ifort
5797 o generate new output.txt files on faulks with g77 & the new -ieee option
5798 checkpoint57c_pre (2005/01/27)
5799
5800 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
5801 update output.txt of exp. global_ocean.90x40x15
5802 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
5803 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
5804 o add saltFlux(+File) forcing capability with periodicExternalForcing
5805 o allow to use pkg diagnostics for GM-Redi & ThSIce output
5806 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
5807 o improvements for the MNC output from DIAGNOSTICS:
5808 - correct handling of the unlimitied dimension
5809 - all dims now have associated coordinate variables
5810 - variables located at U, V, and Corner ("Z") points are now written
5811 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
5812 *all* data points are output
5813 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
5814 o added pkg/seaice/seaice_monitor.F
5815 o mdsio_readfield.F can now read files visible only to master MPI process.
5816 o pkg/seaice: some test code for ice-modified ocean stress
5817 o exf_getffields interpolation defaults to bilinear for all scalar forcing
5818 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
5819 spurious negative numbers for precipitation and humidity. Will cause
5820 some small numerical differences for integrations using pkg/exf/exf_interp.F.
5821 o pkg/ctrl/
5822 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
5823 May be enabled via doPackDiag
5824 * introduce z-scaling of
5825 + gradient (doZscalePack) and
5826 + control (doZscaleUnpack)
5827 o pkg/mdsio/
5828 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
5829 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
5830
5831 checkpoint57b_post (2004/12/20)
5832 o simplify options in diagnostics_fill arguments (remove weird combinations)
5833 o fix MNC coordinate variables so that they now contain per-face index
5834 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
5835 general, EXCH2 grids are only aligned to a "local" coordinate system
5836 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
5837 o Implement instantaneous output within pkg diagnostics:
5838 setting a negative frequency in data.diagnostics produces
5839 "snap-shot" output (as opposed to time-average if freq > 0)
5840 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
5841 NOTE: change ptracer diagnostics name: use 2 characters to work with
5842 more than 9 tracers. Add also diagnostics of advect & diffus flux.
5843 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
5844 becomes the coordinate variable for the 'T' dimension
5845 o add CF-style coordinate variables to MNC
5846 - just a first cut: numbers are meaningless on the cubesphere and
5847 missing along the T axis but otherwise it works!
5848 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
5849 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
5850 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
5851 this is based directly on what the model compute, so that the content of
5852 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
5853 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
5854 o clean up build options files for SunOS, in particular
5855 - remove -traditional from xmakedepend
5856 - change -xarch=v9 to -xarch=native for f77
5857 - restore use of make (not gmake)
5858 - add CC=gcc if using g77
5859 o changes per discussion of AM, JMC, & EH3 today:
5860 - move redundant "grid" variables out of "state" -- in preparation of
5861 creating proper CF-style coordinate variables and in recognition
5862 that any/all grid variables can be easily copied (eg. w/NCO) from
5863 the grid files into any of the other NetCDF files
5864 - *always* output grid variables with MDSIO (this will eventually be
5865 changed)
5866 - output MNC grid file if useMNC is true
5867 o every instance of _END_MASTER() has been found and replaced with
5868 _END_MASTER( myThid ) in order to satisfy certain picky Sun
5869 preprocessors
5870 o re-arrange diagnostics pkg initialisation:
5871 - allow each package to extend the available diagnostics list
5872 - add some checking and fix small problems (multi-threaded, ...)
5873 - new S/R diagnostics_fill (replace fill_diagnostics):
5874 look through the short list of active diag. (instead of the long list)
5875 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
5876
5877 checkpoint57a_post (2004/12/10)
5878 o this set of changes restores TAMC compatibility
5879 tested for global_ocean.90x40x15 adjoint on trough
5880 (what a pain)
5881
5882 checkpoint57a_pre (2004/12/10)
5883 o some modifs in tools/build_options for sunos
5884 o call ctrl_pack for ctrl at end for optimcycle=0
5885
5886 checkpoint57 (2004/12/09)
5887 o add horizontal bi-harmonic viscosity for vertical velocity
5888 - new parameter viscA4W (defaults to viscA4)
5889 - affects only non-hydrostatic code
5890 - to be done: no-slip lateral boundary conditions
5891 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
5892 o implement Implicit Vertical advection for pTracers
5893 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
5894 (implemented also for implicit vertical diffusion & advection)
5895 o OBCS: extend application of tracer open boundary conditions
5896 to a strip beyond the boundary of width Olx/Oly
5897 o add call monitor to TAF set of required calls (flow directives)
5898 and include in natl_box_adjoint
5899 o untangle a few ifdefs related to cost, ctrl, autodiff
5900 untangel a few ALLOW_ECCO_OPTIMIZATION
5901 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
5902 (theta2, salt2 in ecco_cost_weights)
5903
5904 checkpoint56c_post (2004/12/03)
5905 o OBCS as control variables
5906 - update ctrl_ad_diff.list, obcs_ad_diff.list
5907 - remove balance of obcs controls from default
5908 - fix index bug nobcs in ctrl_init
5909 - fix dummy fields filen in ctrl_pack
5910 - add dummy weights for obcs
5911 o lsopt: comment out fort.94 output
5912 o optim:
5913 - remove unnecessary header files
5914 - adjusted namelists
5915 - add xerbla.F to Makefile
5916 o exf:
5917 - multiple modifications of exf_check_range
5918 - unit change in exf_init_runoff from [m/year] to [m/s]
5919 o mdsio:
5920 - i/o-vector change debugLevel from debLevA to debLevB
5921
5922 checkpoint56b_post (2004/12/01)
5923 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
5924 is called from DO_THE_MODEL_IO
5925 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
5926 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
5927 - clean up PTRACERS_WRITE_TIMEAVE a little
5928 o add another verification experiment that tests both the cfc-pkg and
5929 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
5930 reactive tendencies treated inline with regular timestepping
5931 o testreport previously did a lousy job of comparing small numbers, so
5932 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
5933 implemented in the little c-progam tmp_cmpnum.c which is embedded in
5934 testreport.
5935 o ptracers_monitor: bug fix for MPI
5936
5937 checkpoint56a_post (2004/11/28)
5938 o GCHEM: finish reorganizating the package
5939 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
5940 (introduces another 3D-array for each passive tracer, but only if
5941 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
5942 gchemTendency is not needed because the timestep is done separately)
5943 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
5944 - GCHEM is now---more or less cleanly---separate from PTRACERS
5945 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
5946 so clear to me how that should be done in a general way.
5947 o CFC: improve formatting of output in CFC_ATMOS
5948 o PTRACERS:
5949 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
5950 that ALL experiments with ptracers enable can be checked. This makes
5951 GCHEM_MONITOR obsolete.
5952 - include a runtime parameter PTRACERS_monitorFreq that defaults to
5953 monitorFreq
5954 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
5955 o add PTRACERS (PTR0[1-5]) to testreport output
5956 o exf_check_range:
5957 * default changed to .TRUE.
5958 * will check values for niter0 if debLevA, every timestep if debLevB
5959 * STOP in exf_check_range if 'out of range'
5960 * range chosen generous to allow for potential extema
5961 TBD: a version with stricter range
5962 permitted range would be runtime parameters
5963 o GMredi:
5964 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
5965 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
5966 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
5967 o GCHEM:
5968 - move call to GCHEM_FORCING_SEP, so that it is now called before
5969 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
5970 - introduced a useGCHEM runtime flag and applied it everywhere.
5971 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
5972 this flag is now only visible within GCHEM-pkg routines.
5973 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
5974 be replaced by a 3D array that is computed before thermodynamics; for
5975 this, the tracer ID iTracer had to be included into the parameter list
5976 of ptracers_forcing
5977 - set up forward_step to call gchem_forcing, that will replace
5978 gchem_forcing_int in ptracers_forcing
5979 - cleaning up
5980 o small cleaning of exch2: remove files that are also in eesupp/src
5981
5982 checkpoint56 (2004/11/17)
5983 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
5984 o mnc: cleanup "full" files--fixes out-of-memory problem
5985 o ECCO-GODAE
5986 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
5987 * fully merged and updated from SIO code
5988 windstress sign change affects
5989 - exf_inscal_[u/v]stress
5990 - sign of xx_tau[u/v] adjustments
5991 - signs in cost_scat
5992 * ctrl_get_gen: avoid update of tau[u/v] for first few days
5993 * natl_box_adjoint updated and compressed
5994 * 2-level checkpoint switch added
5995 (tested in EXP. 1 of natl_box_adjoint)
5996 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
5997 o SVD
5998 * first complete, non-hacked version for SVD calculations
5999 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
6000 performed via direct access files admtlm_vector.it????
6001 (via ctrl_[un]pack)
6002 * optimcycle is used for ARPACK iteration counter
6003 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
6004 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
6005 and add linear transforms where necessary
6006 * controls are initial/final SST, SSS (can be extended; need to check
6007 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
6008 o mdsio: filename info to both stderr, stdout
6009 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
6010 from sign change
6011
6012 checkpoint55j_post (2004/11/10)
6013 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
6014 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6015 o add consistent build directories and .cvsignore files to verification
6016 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
6017 o make all subroutines 30 or less characters in length for certain older
6018 compilers to work (a thorough search only turns up two routines in
6019 pkg/ptracers)
6020 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
6021 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6022
6023 checkpoint55i_post (2004/10/28)
6024 o change arrays for total vertical diffusivity (2.D if explicit,
6025 3.D if implicit) ; each ptracer uses its own background value.
6026 o added mnc/NetCDF output capability to ocn_compon_interf
6027 - added bits to verification/cpl_aim+ocn so that it can run on
6028 ITRDA and other clusters without the mpirun "-wd" option
6029 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
6030 configuration
6031 o give MNC the ability to create additional files rather than
6032 exceeding a specified file size limit "MNC_MAX_FILESIZE"
6033 - the default is just less than 2GB which is a practical limit
6034 on many systems
6035 o Compute the non-local term using either KPP vertical diffusivity (=default)
6036 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
6037
6038 checkpoint55h_post (2004/10/20)
6039 o add verification test "vermix"
6040 o remove all the *_ioinc flags and replace with the single global
6041 outputTypesInclusive flag
6042 o allow to set a vertical profile of vertical diffusivity for T & S
6043 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
6044 o useMNC moved from data.mnc to data.pkg
6045
6046 checkpoint55g_post (2004/10/14)
6047 o Renaming carbon AD experiments to comply with testreport conventions
6048 o Updating adjoint of Held-Suarez hs94.1x64x5
6049 o Fixing directives for non-ECCO forward_step, after ECCO directives
6050 have been fixed to avoid recomp. of do_oceanic_phys
6051 Works well for global_ocean.90x40x15,
6052 but recomp. issue remains for carbon
6053 o Updating adjoint output for natl_box_adjoint after
6054 pkg/ecco has been modified (see taga c55d_post)
6055
6056 checkpoint55f_post (2004/10/13)
6057 o rename to timeave_init_fixed
6058
6059 checkpoint55e_post (2004/10/13)
6060 o some delicate re-shuffle of store directives to avoid one
6061 extra call of do_oceanic_physics
6062 affects ecco_the_main_loop.F, do_oceanic_physics.F
6063 checkpoint_lev1_directives.h
6064 o NB: this may break global_ocean adjoint temporarily,
6065 but it is clear how to fix it. Will do later, need this now.
6066
6067 checkpoint55d_post (2004/10/11)
6068 o ECCO specific cost function terms (up-to-date with 1x1 runs)
6069 o ecco_cost_weights is modified to 1x1 runs
6070 o modifs to allow observations to be read in as
6071 single file or yearly files
6072 o enable to read exf forcing fields as either
6073 single file or yearly files (flag useExfYearlyFields)
6074 checkpoint55d_pre (2004/10/08)
6075
6076 o switch between 2-level and 3-level checkpointing
6077 o add ability of MNC to write local and "partial" (eg. 2D slices where
6078 the full 3D field is never actually stored) arrays to NetCDF files
6079 with the correct (that is, the complete multi-dimensional) set of
6080 array indicies
6081 - used in mom_vecinv() to write the diagFreq output
6082 - tested (demonstrated) in verification/aim.5l_cs
6083 o further mnc-ification
6084 - add verification/lab_sea to the list with mnc setups
6085 - fix undefined mnc v-names in cd_code
6086 - add kpp to mnc output (both snapshot and timeave)
6087 o non-hydrostatic code
6088 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
6089 in calc_gw.F
6090 - defaults to viscAh
6091 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
6092 friction or Leith) in non-hydrostatic mode, as long as there is
6093 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
6094 o pkg/cost
6095 extend simple cost functions to treat time mean quantities
6096 (T,U,V) via cost_accumulate_state from cost_tile
6097 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
6098 be 2 times larger than the minimum size the advection scheme requires.
6099 now get a perfect conservation of salt in advect_cs test-exp (updated)
6100 o GGL90 (Gaspar's TKE mixed layer)
6101 - add horizontal diffusion of TKE, requires exchanges in
6102 do_fields_blocking_exchanges, horizontal diffusivity is zero by
6103 default. In OPA there is no horizontal diffusion of TKE but the
6104 mixing coefficients are computed from a horizontal average of TKE of
6105 6 points or so. I think that diffusion has a little more physical
6106 justification.
6107 - clean up ggl90_calc in the hope of reducing memory usage (this hope
6108 was in vain)
6109 - mask tke-variable in ggl90_init
6110 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
6111 o fix biharmonic diffusion on CS-grid.
6112 o more obcs stuff
6113 - added obcs_external_fields_load as an alternative to the EXF-pkg option
6114 for reading boundary values. This routine is called from
6115 obcs_prescribe_read
6116 - updated obcs_check
6117 - changed sponge layer relaxation parameter units for days to seconds
6118 - turned off sponge layer by default
6119 - changed argument list of OBCS_CALC to myTime+deltaTclock
6120 - fixed about 35 bugs in obcs_external_fields_load
6121
6122 checkpoint55c_post (2004/09/23)
6123 o obcs stuff
6124 - new runtime flags useOBCSprescribe, useOBCSbalance
6125 - re-arranged obcs_calc
6126 - moved exf_getobcs to obcs_prescibe_read
6127 obcs_prescibe_read is called after ORLANSKI stuff
6128 and independent of it (executable can contain all).
6129 - updated obcs_check
6130 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
6131 These may be necessary only if tangential velocities are
6132 prescribed at OB, not sure, needs testing.
6133 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
6134 which simplifies the calls and passes the ifc check-bounds test
6135
6136 checkpoint55b_post (2004/09/22)
6137 o add a 2D scalar, Z location, exchange_2 routine.
6138 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
6139 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
6140 affects advect_cs results (for the wrong reason): update output.txt
6141 o use a more standard discretization for biharmonic viscosity ;
6142 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
6143 affects results of dome set-up: update output.txt
6144 o fix gad_advection.F (CubedSphere part), back to version 1.23
6145 o fix bug in mom_vi_del2uv.F (CubedSphere part).
6146
6147 checkpoint55a_post (2004/09/20)
6148 o merged code to
6149 * prescribe/read time-dependent open boundaries
6150 (works in conjunction with exf, cal)
6151 * sponge layer code for open boundaries
6152 * each boundary N/S/E/W now has its own CPP option
6153 (healthy for the adjoint)
6154
6155 checkpoint55 (2004/09/17)
6156 o up-to-date adjoint of previous breaks
6157 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
6158 - global_ocean_ebm: adjoint still needs fix (TLM ok)
6159 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
6160 - carbon: * remove tr1-related adjoint verification
6161 * add ptracer as control variable
6162 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
6163 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
6164
6165 checkpoint54f_post (2004/09/16)
6166 o in verification/carbin/ remove experiment related to
6167 ALLOW_PASSIVE_TRACER (array tr1 etc)
6168 code_ad/ input_ad/ results_ad
6169
6170 o add two new packages
6171 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
6172 + subject to optimization (memory)
6173 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
6174 + subject to reordering (many GOTOs in the original code)
6175 + so far opps is called for every (i,j) point, and then operates in
6176 the vertical; one may want to reorder the scheme in order operate in
6177 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
6178 fields)
6179 o overhaul of IO so that we now have flags for MDSIO and/or MNC
6180 - all verification tests compile and run with linux_ia32_g77
6181 - defaults are compatible with current input files--nothing
6182 should change if you were not previously using MNC
6183 - MNC output has been added in numerous places (eg. timeave)
6184 but there are still a few writes not yet do-able with MNC
6185 (this is in progress)
6186 - flags now allow for either/or/both use of MDSIO and MNC and
6187 documentation will soon follow
6188 - numerous small formatting cleanups for ProTeX
6189 o add version info (via BUILD_INFO.h) to MNC and stdout
6190
6191 checkpoint54e_post (2004/09/02)
6192 o add two new packages
6193 - pp81 (Packanowski and Philander, 1981), Richardson number and
6194 stratification dependent mixing
6195 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
6196 - these scheme operate in a similar manner as KPP (without ghat, of
6197 course), however there is only one diffusivity that is used for both
6198 temperature and salinity (and passive tracers)
6199 o add offline package
6200 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
6201 provided by Stephanie Dutkiewicz
6202 o genmake2: add ability to search for C compilers and cleanup test output
6203 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
6204
6205 checkpoint54d_post (2004/07/27)
6206 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
6207 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
6208 leading to additional shift by 5 days each year of integration
6209 (i.e. leading to considerable offset over the years)
6210 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
6211 o start with no AB and no initial filtering (staggerTimeStep):
6212 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
6213 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
6214 (external loading & cpl import/export stay in forward_step.F)
6215 o update coupling interface to work with new staggerTimeStep
6216 o change MDSIO ptracers_pickup.
6217 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
6218 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
6219 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
6220
6221 checkpoint54c_post (2004/07/18)
6222 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
6223 this affects (truncation error) output.txt of test-exp:
6224 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
6225 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
6226 o change Qnet to always be the net heat flux, (+upward).
6227 affects (truncation error) output of natl_box exp.: updated
6228 o define the max number of passive tracers in PTRACERS_SIZE.h
6229 o start to test mnc routinely in exp0
6230 o add sea-ice loading (sIceLoad) as a new forcing field.
6231
6232 checkpoint54b_post (2004/07/08)
6233 o add testreport "-j JOBS" option for parallel builds (tested and pretty
6234 impressive on Altix and Opteron systems)
6235 o diagnostics can now write NetCDF files through the mnc package
6236 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
6237 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
6238 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
6239 affects (truncation error) output of lab_sea & natl_box exp.: updated
6240 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
6241
6242 checkpoint54a_post (2004/07/06)
6243 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
6244 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
6245 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
6246 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
6247 + internal_wave (shift in writing cg2d_ini_res)
6248 checkpoint54a_pre (2004/07/05)
6249
6250 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
6251 - modified verification/lab_sea and natl_box_adjoint accordingly
6252
6253 checkpoint54 (2004/07/02)
6254 checkpoint53g_post (2004/07/02)
6255 o prepare splitting of thermodynamics: store convect.counter in common block
6256 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
6257 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
6258 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
6259 o new parameter "nShapS": allow to treat differently S from T (nShapT)
6260 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
6261 o restore adjointability
6262
6263 checkpoint53f_post (2004/06/25)
6264 o modifications that affect AIM experiment results (update output.txt):
6265 - no advection of S at top interface Nr (pkg/generic_advdiff)
6266 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
6267 o AIM pkg:
6268 - include stability function into surf.Flux derivative relative to Tsurf
6269 - calculate clear-sky radiation & surface temp. change (for diagnostics)
6270
6271 checkpoint53e_post
6272 o merged cylindrical coord configuration
6273 o added rotating_tank experiment
6274 checkpoint53e_pre
6275
6276 checkpoint53d_post (2004/06/14)
6277 o faulks upgraded: re-generate output.txt that have changed:
6278 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
6279 o Added Bryan and Lewis, 1979, vertical diffusivity profile
6280 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
6281 o added Sadourny discretization of Coriolis
6282 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
6283 - re-enabled use of omega3 (useAbsVorticity)
6284 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
6285 vector-invariant equations
6286 - note: does *NOT* yet use same variable visc. for no-slip BC's.
6287 o recoded the lateral boundary conditions for non-hydrostatic w, this time
6288 hopefully without new bugs
6289 - still to do: biharmonic friction for non-hydrostatic w
6290 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
6291 o regenerated output for global_ocean_ebm (using -ieee)
6292 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
6293 of mom_common/
6294 - simple re-arrangement of instructions within computing loop
6295 checkpoint53d_pre (2004/05/21)
6296
6297 checkpoint53c_post (2004/05/21)
6298 o new version of coupler for AIM+thSIce and Ocean models
6299 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
6300 - land: change Evaporation of snow
6301 - aim with thSIce: fix bug in snow-precip.
6302 o changes to calc_gw.F
6303 - bug fix for w^2 term near the bottom boundary
6304 - (hopefully) improve the lateral slip boundary condtions for use with
6305 partial/looped cells
6306 - because the bug fix changes two verification experiments anyway (exp5
6307 and plume on slope), change the lateral boundary condition from half slip
6308 to the value of no_slip_sides
6309 o ebm package wasnt quite up to the parallel task. Fixed that.
6310 o Adjoint of EBM package + verification
6311 * TLM OK
6312 * ADM not sufficient accuracy yet (needs further testing)
6313
6314 checkpoint53b_post (2004/05/14)
6315 o Commiting new energy balance model to repository
6316 * package is pkg/ebm
6317 * verif. is verification/global_ocean_ebm
6318 * references are in ebm_driver.F
6319 C * X. Wang, P. Stone and J. Marotzke, 1999:
6320 C Global thermohaline circulation. Part I:
6321 C Sensitivity to atmospheric moisture transport.
6322 C J. Climate 12(1), 71-82
6323 C * X. Wang, P. Stone and J. Marotzke, 1999:
6324 C Global thermohaline circulation. Part II:
6325 C Sensitivity with interactive transport.
6326 C J. Climate 12(1), 83-91
6327 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
6328 C Destabilization of the thermohaline circulation
6329 C by atmospheric eddy transports.
6330 C J. Climate 7(12), 1870-1882
6331 o Will need long integration testing.
6332 checkpoint53b_pre (2004/05/14)
6333
6334 o created pkg/mom_common in preparation for variable viscosity code
6335 o renamed and split ini_mnc_io
6336 o pkg/land: only liquid water can diffuse or run-off
6337 o AIM using land: soil wetness availability account for snow
6338 o added printMapIncludesZeros to EEPARMS namelist
6339
6340 checkpoint53a_post (2004/05/11)
6341 o restore TAMC compatiility for exf_constants.h
6342 (no usage of _d in .h)
6343 o Additional storing in KPP in an attempt to fix
6344 TAMC problem with adjoint of KPP code.
6345 (no success...)
6346 Identical code works fine with TAF.
6347 o Fixed verification/natl_box_adjoint experiments.
6348 Initial conditions for Experiments 4 and 5 are now
6349 set to "SEAICE_initialHEFF=0", which is more reasonable,
6350 and hence gives results closer to that of Experiment 2.
6351 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
6352
6353 checkpoint53 (2004/05/06)
6354 o stable checkpoint with up to date adjoint
6355 TLM tests only run for 1st grdchk at the moment. Its unclear if
6356 this is a code problem or a problem with resetting code for g_
6357 variables that is being autogenerated wrong.
6358 Otherwise:
6359 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
6360 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
6361 are both still in chaos following their security messes.
6362
6363 checkpoint52n_post (2004/05/06)
6364 o various build (mostly genmake2) changes including:
6365 - ability to build/run more easily within Cygwin and MacOS X
6366 - more complicated Makefiles with a stronger dependence on Gnu Make
6367 o pkg/seaice modifications
6368 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
6369 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
6370 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
6371 - changed proxy for geostrophic velocity and updated
6372 verification/lab_sea/results/* accordingly
6373 - removed ADI dynamic solver from pkg/seaice
6374 - replaced all occurrences of 1/CSTICE or 1/CSUICE
6375 they caused a segmentation fault under certain circumstances
6376 - removed unused field WATR
6377 o bug fix in exf-package:
6378 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
6379 now reflect that.
6380 o small fixes in the cal-package:
6381 - set reference date to first of January for the 'model'-calendar
6382 - failing of cal_CheckDate in cal_FullDate now actually results in a
6383 warning
6384 o small modifications in exf-package to increase flexibility:
6385 - change climtempfreeze from a constant to a runtime parameter that
6386 is specified in data.exf_clim (default = -1.9)
6387 - introduce runtime parameter windstressmax (default = 2.0) that is
6388 specified in data.exf
6389 o fix in pkg/thsice:
6390 - update Evap (Tsf changes) to be consistent with Latent heat flux
6391 - maintain snow precipitation unchanged (even if Tsf >=0).
6392 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
6393
6394 checkpoint52m_post (2004/04/18)
6395 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
6396 this does not change any of the results, because myIter=0 in swfrac always
6397 lead to jwtype=2 (the default anyway), but the call makes little sense
6398 as a default
6399 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
6400 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
6401 atmospheric model (AIM) to use it ; add a "slab ocean" component.
6402 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
6403 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
6404 o extending useSingleCpuIO option to work with new exch2 I/O format
6405 - old-style, missing-tile I/O is still accessible by defining CPP
6406 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
6407 o monitor package can write to NetCDF files and/or STDOUT
6408 o fix re-definition bug in MNC_GRID_INIT_ALL()
6409 o doc/api_reference added
6410 - a framework for building an API Reference Manual using all
6411 the "protex" comments embedded in the code
6412 - see pkg/generic_advdiff, pkg/mnc for examples
6413 o MNC:
6414 - make myThid the last argument for all subroutines
6415 - new default for the grid files: NO halos
6416 - add useMNC and other run-time flags
6417 - separate per-file-group handling of the unlimited dimension
6418 - early initialization of MNC w/ flags read at the eeboot stage
6419 and lookup tables set in initialize_fixed
6420 - write all MNC output to a freshly-created directory
6421 o thermodynamics sea-ice (thsice) is now tested with testreport.
6422 o test exp. advect_cs: use the standard cs32 grid ; update output.
6423 o Added functionality to grdchk:
6424 pick global i,j,k position (or nearest wet) where to perform check.
6425
6426 checkpoint52l_post (2004/03/11)
6427 o new land formulation:
6428 a) use ground enthalpy as prognostic variable to ensure exact
6429 energy conservation.
6430 b) account for water temperature and for latent heat of freezing
6431 in all processes (rain, run-off, ground storage)
6432 c) compute surface and ground temperature implicitly.
6433 o aim_v23 modification for new land model:
6434 a) Treat separately land / ocean / sea-ice surface fluxes
6435 to allow implicit computation of land & sea-ice surface temp.
6436 b) add snow precipitation.
6437 checkpoint52l_pre (2004/03/11)
6438
6439 o fix problem (when 1 tile is empty) in min/max monitor.
6440 o fix bug in timeAve (u,vZetatave in common block)
6441 o no restoring terms under ice for pkg/seaice
6442 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
6443 o bug fix for pkg/seaice pickups
6444 o change MNC call locations and add coordinate attributes
6445 o mask vorticity at the corner ; affects global_ocean.cs output
6446 o fix ini_curvilinear_grid ; test CS experiments with mpi
6447 o aim.5l_cs: modify sea-ice fraction input file ; update output
6448 o exf: Adding simple range check routine for exf fields after read
6449
6450 checkpoint52k_post (2004/02/23)
6451 o removed top-level directory "diags"
6452 - we migrated these functions to pkg/timeave a long time ago
6453 o fixed bug introduced in pkg/monitor
6454 o accuracy ctrlprec = 32 insuffient for gradient checks using
6455 averaged fields (I/O via cost_averages)
6456 -> use ctrl.h in active_file*.F to control I/O precision.
6457 o paramter list of CALL ADTHE_MAIN_LOOP
6458 o added initial do_the_model_io to ecco
6459 o set all ...Freq to zero after cost_final
6460 taveFreq, dumpFreq, pChkptFreq
6461 o MAIN and ECCO differentiability restored
6462
6463 checkpoint52j_post (2004/02/18)
6464 o fix nchklev in tamc.h for global_ocean...
6465 o Bringing flow and store directives up-to-date
6466 o Really weird thing!
6467 call do_the_model_io from the_main_loop with parameters
6468 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
6469 TAF places a faulty re-call of initialise_varia
6470 after cost_final call which should not be there!
6471 checkpoint52j_pre (2004/02/03)
6472
6473 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
6474 error messages
6475 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
6476 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
6477 debug output
6478 o modfied mdsio_writefield.F to handle non-global files under exch2
6479 o update AIM Cubed-Sphere exp (aim.5l_cs):
6480 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
6481 o update AIM Equatorial Channel exp:
6482 use standard aim_v23 pkg and change the SST fields to be more realistic.
6483 o globalFile now works with exch2
6484 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
6485 mon_vort3.F to make exch2 friendly with >1 tile per cube face
6486 o limit timeave output for hi-res integrations
6487
6488 checkpoint52i_post (2004/01/21)
6489 o removed CPP_EEOPTIONS.h from verification/*/code
6490 o updated the tiling for global_ocean_pressure
6491 checkpoint52i_pre (2004/01/20)
6492
6493 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
6494 the old pkg/aim).
6495
6496 checkpoint52h_pre (2004/01/20)
6497 o shortened offending lines in exch2_send_rx?.template
6498 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
6499 o genmake2: add build & execute test for NetCDF code
6500 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
6501 old grid files, moved CPP_EEMACROS.h to pkg/exch2
6502 o added useSingleCPUIO flag to monitor.F and mon_out.F
6503 o added temporary hack for sea-ice dynamics on the cube:
6504 metric terms are ignored and it is assumed that
6505 there is no sea-ice on cube faces 1, 2, 4, and 5.
6506
6507 checkpoint52f_post (2004/01/09)
6508 o added exch2 cube routines to pkg/exch2
6509 o modified hs94.cs-32x32x5 to use it
6510 o added new grid files to hs94.cs-32x32x5
6511 checkpoint52f_pre (2004/01/07)
6512
6513 checkpoint52e_post (2004/01/07)
6514 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
6515 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
6516 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
6517 to work with implicit vertical advection and AB ;
6518 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
6519 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
6520 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
6521 checkpoint52e_pre (2004/01/02)
6522
6523 o fix bug in impldiff when Nr=1 or Nr=2.
6524 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
6525 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
6526 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
6527 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
6528 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
6529 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
6530 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
6531
6532 checkpoint52d_post (2003/12/16)
6533 o re-tiled many expts to allow comparison in multi-processor mode
6534 - updated output accordingly
6535 - changed hs94.128x64x5 to use intial T from file rather than use the
6536 random number generator
6537 o add infrastructure in model routines for fizhi and gridalt packages
6538 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
6539 o changes to permit hi-res, cubed-sphere, configuration
6540 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
6541 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
6542 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
6543 of surface winds for the cube
6544 (A verification experiment, based on global_ocean.cs32x15, but with
6545 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
6546 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
6547 complete with example surface forcing files and matlab scripts to look
6548 at the output and compare it with that of global_ocean.cs32x15.)
6549 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
6550 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
6551 to conform to the common rule.
6552 o check-in the first version of the coupler + interfaces for multi-components
6553 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
6554 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
6555 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
6556 - ocean and atmos. share the same horizontal grid (no interpolation).
6557 - exchanges between component and coupler is done in forward_step
6558 o new verification experiment, cpl_aim+ocn:
6559 coupled ocean - AIM atmosphere on cs32 grid.
6560
6561 checkpoint52d_pre (2003/12/06)
6562 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
6563 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
6564
6565 checkpoint52c_post (2003/11/25)
6566 o Fixing OPTIONS files for use of exf:
6567 - ALLOW_ECCO not needed
6568 - ECCO_CPPOPTIONS.h should not be included from
6569 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
6570 as has been the case in the past
6571 - All cal/exf related options are currently set in
6572 single header file. Should remain so until we
6573 agree on a consistent new policy.
6574 o Removed all CPP options for cal package.
6575 cal has no more CPP options.
6576 o modified STOREs in GAD_ADVECTION
6577 o corrected key comp. for passkey
6578
6579 checkpoint52b_post (2003/11/23)
6580 o new version: "thsice" of thermodynamic sea-ice pkg:
6581 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
6582 - modify fluxes but do not change theta directly;
6583 - light cleaning of bulk_force pkg (still needed with thsice).
6584 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
6585 + output_thsice.txt to test thsice & bulk_force pkgs.
6586 o put back grid & coriolis monitor output.
6587 checkpoint52b_pre (2003/11/23)
6588
6589 o call "do_the_model_io" at the beginning (=> dump initial state)
6590 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
6591 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
6592 (need info on NUMBER_OF_PTRACERS)
6593 o missing PTRACERS headers in some routines
6594 o default tamc.h in pkg/autodiff supposed to crash
6595 to ensure proper customization
6596
6597 checkpoint52a_post (2003/11/17)
6598 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
6599 - moved surfaceTendencyTice from pkg/seaice to main code
6600 - subroutine FREEZE_SURFACE now limits only surface temperature
6601 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
6602 => new output.txt for global_ocean.cs32x15 & global_with_exf
6603 - keep the old version of FREEZE for backward compatibility;
6604 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
6605 - corresponding modifs for TAF directives
6606 o added surface flux output variables to TIMEAVE_STATVARS
6607 o time-averaged output for pkg/ptracers
6608 o fix problem with ECCO-related divided adjoint
6609 snapshot file was missing some ad-variables,
6610 but no warning issued by TAF
6611
6612 checkpoint52a_pre (2003/11/12)
6613 o some bug fixes for #undef REAL4_IS_SLOW
6614
6615 checkpoint52 = ecco_c52_e35
6616 o after testing adjoints of checkpoint51u_post
6617
6618 checkpoint51u_post (2003/11/06)
6619 o this is the post-merge tag of the ecco-branch
6620 (needs another clean checkout and re-testing)
6621 o various natl_box_adjoint configs and results
6622 but no input fields
6623 o obcs adjoint not yet merged!
6624 o adding ECCO global 1x1 and 2x2 degree configs
6625 o updated/extended some store directives for seaice
6626 o pkg/ecco now containes ecco-specific part of cost function
6627 o top level routines the_main_loop, forward_step
6628 supersede those in model/src/
6629 previous input data.cost now in data.ecco
6630 (new namelist ecco_cost_nml)
6631 o in ctrl/ cleaned some cross-dependencies and updated CPP options
6632
6633 checkpoint51t_post (2003/11/04)
6634 o this is the pre-merge tag of the ecco-branch
6635
6636 checkpoint51s_post (2003/11/04)
6637 o cleanup: removed various obsolete #define-s
6638 o pkg/grdchk
6639 - renamed 'ph-grd 3' to 'grad-res'
6640 - merged from ecco-branch
6641 (remaining bug fixes for obcs gradient checks)
6642 - additional high-precision output for testreport
6643 (grep for 'precision_grdchk_result')
6644
6645 checkpoint51r_post (2003/11/03)
6646 o cleaned up or removed CPP_OPTIONS.h files
6647 o updated results for some of the tests to reflect the new
6648 optfiles (-ieee: -O0 instead of -O3)
6649
6650 checkpoint51q_post (2003/10/30)
6651 o cd_code:
6652 - moved cd_scheme.F -> cd_code_scheme.F
6653 - separate read_checkpoint from cd_code_ini_vars.F
6654 - separated cd_code part from write_checkpoint
6655 - updated AD_SOURCE, generated .flow
6656 - added CD_CODE_VARS.h to the_main_loop
6657 - Moving cd_code specific store dir.s to pkg/cd_code
6658 o ctrl package totally restructured
6659 - pack/unpack now optional and decoupled from
6660 xx_/adxx_ I/O
6661 - ctrl_pack/unpack cleaned
6662 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
6663 - confined inclusion of AD_CONFIG.h to where necessary.
6664 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
6665
6666 checkpoint51p_post (2003/10/30)
6667 o create initial cd_code package
6668 - WARNING: the initialization of fields within packages
6669 is broken because INI_FIELDS (where READ_CHECKPOINT is
6670 called) is called *before* PACKAGES_INIT_VARIABLES.
6671 This seems to be backwards since
6672 1) its important to initially zero the entire field including
6673 the "halo" region
6674 2) zeroing needs to be done *before* reading pickup info
6675 and the pickup call might or might not happen in any
6676 particular run
6677 - this needs an overhaul for R2
6678 o cleanup verification/*/code/GMREDI_OPTIONS.h
6679 o cleanup testreport
6680
6681 checkpoint51o_post (2003/10/27)
6682 o bringing AD-related verif's up to date with genmake2
6683 - carbon/
6684 - global_ocean.90x40x15/
6685 - hs.94.1x64x5/
6686 - (front_relax/ )
6687 o (more) consistent directory structure for AD-related verif.'s
6688 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
6689 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
6690 o bug fix in find_alpha.F for MDJWF:
6691 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
6692 change rho -> rho-rhoConst
6693 - replace call find_rho to find_rhonum
6694 o initialisation of rFlx extended to full array (required by TAF)
6695 and shifted to thermodynamics
6696 o removed PTRACERS.h in ptracers routine
6697 o added surfacetendencyPtr to S/R parameter list pracers_forcing
6698 o Correcting initialisations for fVerU, fVerV.
6699 o helping TAF to recognize dependency on kUp for
6700 fVerU, fVerV
6701 o Replacing delZ by delR in pkg/ctrl/
6702 checkpoint51o_pre (2003/10/24)
6703
6704 o undid all of cp51 pending some cleanups and discussion
6705 o added the [#include "AD_CONFIG.h"] statement to all files that need
6706 it for adjoint/tl #defines
6707 o re-worked the build logic in genmake2 to support AD_CONFIG.h
6708 o removed tools/genmake since it no longer works
6709
6710 checkpoint51n_post (2003/10/23)
6711 o modifications to make FREEZE flux visible to pkg/kpp
6712 - moved surfaceTendencyTice from pkg/seaice to main code
6713 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
6714 - subroutine FREEZE now limits only surface temperature
6715 (this means new output.txt for global_ocean.90x40x15,
6716 global_ocean.cs32x15, and global_with_exf)
6717 o added surface flux output variables to TIMEAVE_STATVARS
6718
6719 checkpoint51n_pre (2003/10/23)
6720 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
6721 o added [#include "AD_CONFIG.h"] to all files that use the following
6722 defines:
6723 - ALLOW_ADJOINT_RUN
6724 - ALLOW_TANGENTLINEAR_RUN
6725 - ALLOW_ECCO_OPTIMIZATION
6726
6727 checkpoint51m_post (2003/10/21)
6728 o incorporating changes to get TAMC/TAF working in genmake2
6729 - added new TAMC/TAF targets to the Makefile
6730 - various cleanups related to package handling
6731 - these changes should have no impact on the forward model
6732
6733 checkpoint51l_post (2003/10/20)
6734 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
6735 - faster algorithm for cal_addtime.F
6736 - higher precision arithmetic, where needed
6737 - pkg/exf *startdate variables changed from calendar date to
6738 model integration time
6739
6740 checkpoint51l_pre (2003/10/17)
6741 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
6742 o enable to apply restoring on S & T only in a latitude band.
6743 o update output (external_forcing_surf modif. change truncation errors)
6744 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
6745
6746 checkpoint51k_post (2003/10/16)
6747 o change default to: useNHMTerms=.FALSE.
6748 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
6749 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
6750 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
6751 exp1, ideal_2D_oce
6752 - change data file of oceanic exp (leave the results unchanged for now)
6753 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
6754 o set gravitySign automatically according to the vertical coordinate used
6755 (and change sign: back to "logical" value: +1 when R increases downward)
6756 o added an include barrier to the default CPP_OPTIONS.h and
6757 removed the #include "PACKAGES_CONFIG.h" from it
6758 o fix a bug in mom_fluxform (from chk51j_post)
6759
6760 checkpoint51j_post (2003/10/10)
6761 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
6762 o adjusted some flow directives (dynamics, thermodynamics)
6763 o added cubed-sphere case to test cost function
6764 o heckpoint_lev?_directives.h now include
6765 pkg-specific directives, whenever those are enabled.
6766 o Moving pkg-specific flow directives to corresponding pkg
6767 Moving pkg-specific differentiation list to corresponding pkg
6768 Moving pkg-specific checkpoint-lev storing to corresponding pkg
6769 ---> conventions are
6770 - pkg_ad.flow
6771 - pkg_ad_diff.list
6772 - pkg_ad_check_lev?_dir.h
6773
6774 checkpoint51i_post (2003/10/09)
6775 o merge of the branch-genmake2
6776 - knowingly breaks the older genmake
6777 - automatic generation of all ALLOW_${PKG_NAME} defines
6778 - new testreport supersedes older testscript
6779 o large number of package inclusion and header cleanups
6780 checkpoint51i_pre (2003/10/08)
6781
6782 o new output for adjoin of global ocean vector invariant
6783 o fix for checkpoint of thermodynamic seaice and bulk_force
6784 o Steph gchem various cleanups
6785
6786 checkpoint 51h_pre
6787 o fixed some single quotes
6788 o modify gchem pkg to be more versatile
6789 o modifications to clean up dic pkg
6790 o add pkg/cfc
6791
6792 checkpoint51g_post (2003/10/02)
6793 o provide links for ARPACK and ADM*TLM
6794 o start removing verification/vero/
6795 o update AD-related stuff
6796 (in particular some IF-statements in model/src/ routines)
6797 o adding to verification/global_ocean.90x40x15/ adjoint of
6798 vector invariant setup
6799
6800 checkpoint51f_post (2003/10/02)
6801 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
6802 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
6803 of tracer Green's fucntions for ocean inversion project.
6804
6805 checkpoint51f_pre (2003/08/07)
6806 o Added on-the-fly spatial interpolation capability
6807 "USE_EXF_INTERPOLATION" to pkg/exf.
6808 - This is a temporary Cartesian-grid hack until
6809 the super-duper ESMF coupler becomes available.
6810 - See verification/global_with_exf/README for usage example.
6811 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
6812 flags and modified pkg/seaice accordingly.
6813 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
6814 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
6815 non-local transport term.
6816
6817 checkpoint51e_post (2003/08/03)
6818 o pkg/mom_vecinv:
6819 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
6820 - add time-ave diagnostic of vorticity advection.
6821 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
6822 o atmospheric geopotential: - include water vapor effect;
6823 - use p^kappa in p* scaling.
6824 o land pkg: read initial state from files.
6825 o AIM : add stratospheric drag in the upper level
6826
6827 checkpoint51d_post (2003/07/18)
6828 o change function ILNBLNK (=> last non-blank char.) to return zero
6829 (instead of the string length) when the string. char is empty
6830 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
6831 o modif's to restore TAMC compatibility
6832 - avoid "_d" constructs in PARAMETER declarations
6833 - avoid interrupting lines by comment lines
6834 o Use cluster local disks for purely local I/O
6835 vs. globally visible disks needed for ctrl stuff
6836 (merged from ecco-branch)
6837 - new active_file_loc... and mdsio_..._loc routines
6838 - affected packages: autodiff, ctrl, grdchk, mdsio
6839
6840 checkpoint51c_post (2003/07/08)
6841 o introducing integer flag debugLevel
6842 - debLevZero: suppress all output
6843 - debLevA: standard
6844 - debLevB: equivalent to current debugMode=.TRUE.
6845 o introducing pathname variable mdsioLocalDir for mdsio
6846 that can be specified at runtime
6847 (relevant for cluster I/O to local disk)
6848 `
6849 >>>checkpoint51b_post
6850 adjoint of ptracers
6851 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
6852 o extended state in checkpoint_lev?, etc.
6853 o alternative ctrl/cost with tr1 or ptracer
6854 o new comlev1_bibj_ptracers
6855 o new ptracers.flow
6856 o made ptracers_forcing same as external_forcing_s
6857 o added verification for adjoint with ptracers
6858 - adm. grdchk fail so far
6859 - tlm. grdchk OK
6860 - checked tapelev/comlev recomputations: OK
6861 <<<checkpoint51b_pre
6862
6863 checkpoint51a_post (2003/06/25)
6864 o added code for biogeochemistry package
6865 - new pkgs: dic, gchem
6866 - new subroutine in ptracers
6867 o modify code for biogeo packages
6868 - in model/src and pkg/ptracers
6869
6870 checkpoint51 (2003/06/24)
6871 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
6872 - autodiff, ctrl, exf, grdchk, seaice
6873 kept separate packages
6874 - cost, ecco, obcs
6875 o updating verification/internal_wave, verification/lab_sea
6876 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
6877
6878 checkpoint50i_post (2003/06/23)
6879 o Preparing next differentiable checkpoint and sync
6880 of MAIN vs. ecco-branch
6881 - 1st step: this one is differentiable
6882 - 2nd step: next(! not this) checkpoint will have updated packages
6883 from ecco-branch)
6884
6885 checkpoint50h_post (2003/06/20)
6886 o new package "land": provide surface BC for AIM.
6887 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
6888 o AIM: use true log-P extrapolation for near surface temp (= as in
6889 F.Molteni paper) ; update aim.5l_cs output.
6890 o New variable in PARM03 for more flexible pickups
6891 o somewhat cleaned package initialisation sequence for
6892 ctrl/ cost/ ecco/ in packages_... routines
6893
6894 checkpoint50g_post (2003/05/23)
6895 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
6896 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
6897 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
6898 made the default because of faster convergence than ADI
6899
6900 checkpoint50f_post (2003/05/23)
6901 o exf totally restructured
6902 - replaced all exf_set_ routines by one generic exf_set_gen.F
6903 and made sure it's still differentiable
6904 - split exf_getffields.F into new exf_bulkformulae.F
6905 - exf_inscal_/exf_outscal_ suffixes consistent with field names
6906 - updated adjoint/makefile and relevant verif. accordingly
6907
6908 checkpoint50f_pre (2003/05/23)
6909 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
6910 + change Evap over land. (update aim.5l_cs output)
6911 o added missing .cvsignores and made uniform across expts
6912 o changed configuration of tidal_basin_2d expt
6913 o added pkg/debug functions for tracing code in fatal crashes
6914 o tidied pkg/monitor to use MONITOR_OPTIONS.h
6915 o new fn in pkg/monitor to stop model if solution grows too big
6916 o removed lots of single quotes from comments
6917
6918 checkpoint50e_post (2003/05/14)
6919 o make KPP work with PTRACERS
6920 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
6921 nearly a copy of kpp_transport_s
6922 - there is no analogue to SurfaceTendencyS, so I have to use
6923 gPtr(of the surface layer) instead
6924 o add a new platform SunFire+mpi (SunFire 15000) to genmake
6925 checkpoint50e_pre (2003/05/13)
6926
6927 checkpoint50d_post (2003/05/13)
6928 o change kpp output from multiple-record state files to single-record state
6929 files analogous to write_state.F
6930 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
6931 analogous to the cg2d-related output.
6932 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
6933 so that writing to internal file fn (with length 512) fails.
6934 checkpoint50d_pre (2003/05/12)
6935
6936 checkpoint50c_post (2003/05/12)
6937 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
6938 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
6939 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
6940 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
6941 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
6942
6943 checkpoint50c_pre (2003/04/30)
6944 Merging from release1_p13:
6945 o bug fix for pkg/seaice dynamic solver
6946 o Added SEAICE_initialHEFF to pkg/seaice
6947
6948 checkpoint50b_post (2003/04/17)
6949 o store u*,v* in gU,V instead of in guNm1,gvNm1
6950 o in order to put the momForcing out of the Adams-Bashforth:
6951 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
6952 to timestep.F
6953 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
6954 o re-generate output for highly sensitive test-exp:
6955 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
6956
6957 checkpoint50b_pre (2003/04/17)
6958 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
6959 o corrected CPP option mismatch in exf_Bulk... functions for case
6960 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
6961
6962 checkpoint50a_post (2003/03/21)
6963 o Bug fix for merging between c50 and KPP.
6964 ikey was passed from thermodynamics to kpp_calc via
6965 common block rather than being recomputed in kpp_calc,
6966 in contradiction with new key itdkey.
6967 New key ikppkey created, and tamc.h headers updated.
6968
6969 checkpoint50 (2003/03/08)
6970 - 2nd step of merge with ecco-branch:
6971 merge changes in ecco-branch back into main trunk
6972 - bug fix in find_alpha
6973 - more storing in gmredi_calc_tensor.F, kpp_routines.F
6974 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
6975 - merged some sliced AD support routines
6976
6977 checkpoint49 (2003/03/06)
6978 merged from ecco-branch:
6979 o exf:
6980 - Enable initialisation of forcing fields to constant
6981 (runtime) values.
6982 - in exf_getffields.F
6983 Reduce i-/j-loop to interior domain, discarding overlaps.
6984 That also fixes wrong TAF-key computations for key_1, key_2
6985 with bulf formulae.
6986 - exf_init.F modify #ifdef for exf_init_evap
6987 - exf_getffieldrec.F, ctrl_getrec.F
6988 The following INT-usages are not safe:
6989 fldsecs = int(fldsecs/fldperiod)*fldperiod
6990 fldcount = int(fldsecs/fldperiod) + 1
6991 and were modified.
6992 o autodiff: checkpoint_lev...
6993 - updated storing for bulk formulae (some arrays were missing)
6994 - added state for seaice package
6995 - synchronized with main branch
6996 o DIVA:
6997 Modif.s in
6998 - the_main_loop.F
6999 - the_model_main.F
7000 and added cost_final_restore.F cost_final_store.F
7001 o With these changes, it is possible to fully separate
7002 the first forward run to compute the cost function (mdthe_main_loop)
7003 and adjoint runs over individual DIVA intervals (adthe_main_loop)
7004 into separate model executions.
7005 This enables better tuning of DIVA to given queue sizes.
7006 o Loss of cost function value in consecutive DIVA runs is
7007 fixed by storing to 'costfinal' file.
7008 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
7009 beginning/end of adjoint integration is accounted for.
7010 The current changes apply to TAF-1.4.26.
7011 TAF has one remaining bug, requiring one manual change
7012 (see MITgcm manual).
7013 o cal: synchronized between MAIN and ecco-branch
7014
7015 checkpoint48i_post (2003/03/05)
7016 o Changes to restore differentiability of code w.r.t. previous tag
7017 (mostly adding new routines to make list and replacing
7018 pressure by totPhiHyd).
7019 o Updated and merged grdchk package
7020 - has both ADM and TLM checks
7021 - works for single- and multi-proc.
7022 - output cleaned
7023 - worked successfully for parallel DIVA
7024 o genmake:
7025 - Adding -platform=SP4
7026 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
7027 o Modif. for DIVA:
7028 ctrl_unpack should not be called in intermediate DIVA interval.
7029 (similar thing would apply for active files such as
7030 tbar, sbar, psbar, which should not be reinitialised;
7031 only relevant for ecco-branch)
7032
7033 checkpoint48h_post (2003/02/28)
7034 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
7035 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
7036 o Added SEAICE_initialHEFF to pkg/seaice
7037 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
7038
7039 checkpoint48g_post (2003/02/18)
7040 --- EOS:
7041 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
7042 store total Potential in totPhyHyd for diagnostics & EOS.
7043 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
7044 --- Pressure/geopotential gradient:
7045 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
7046 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
7047 ( changes results of global_ocean_pressure )
7048 o NLFS + z-coord.: add eta*Rho' contribution.
7049 o accurate phiHyd when using interface-W at the middle between 2 centers
7050 ( changes results of ideal_2D_oce )
7051 o includes r* 2nd term in potential gradient.
7052
7053 checkpoint48f_post (2003/02/18)
7054 Merging from release1_p12:
7055 o Modifications for using pkg/exf with pkg/seaice
7056 - improved description of the various forcing configurations
7057 - added basic radiation bulk formulae to pkg/exf
7058 - units/sign fix for evap computation in exf_getffields.F
7059 - updated verification/global_with_exf/results/output.txt
7060 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
7061 (SBO) core products, including oceanic mass, center-of-mass,
7062 angular, and bottom pressure (see pkg/sbo/README.sbo).
7063 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
7064 to avoid negative values in shallow regions.
7065 - updated verification/natl_box/results/output.txt
7066 - updated verification/lab_sea/results/output.txt
7067 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
7068 o Added useSingleCpuIO option (see PARAMS.h).
7069 o Updated useSingleCpuIO option in mdsio_writefield.F to
7070 work with multi-field files, e.g., for single-file pickup.
7071 o pkg/seaice:
7072 - bug fix in growth.F: QNET for no shortwave case
7073 - added HeffFile for specifying initial sea-ice thickness
7074 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
7075 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
7076 kpp_transport_t.F, forward_step.F, and the_main_loop.F
7077 o pkg/seaice:
7078 - adjoint-friendly modifications
7079 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
7080
7081 checkpoint48e_post (2003/02/12)
7082 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
7083 o dynamics: change definition of computational domain & adapt mom_fluxform
7084 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
7085 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
7086 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
7087 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
7088 global_ocean.90x40x15 global_with_exf global_ocean_pressure
7089 inverted_barometer solid-body.cs-32x32x1
7090 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
7091
7092 checkpoint48d_post (2003/02/09)
7093 o in preparation for r*:
7094 a) use pre-computed gradient of hydrostatic potential:
7095 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
7096 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
7097 => affects results of glob_oce_pressure (different truncation error)
7098 update output.txt of ideal_2D_oce & global_ocean_pressure
7099
7100 checkpoint48d_pre (2003/02/08)
7101 o in preparation for r*:
7102 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
7103 pass the 2 comp. of the grad. as arguments to momentum S/R.
7104 but for the moment, only used if it does not change the results.
7105 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
7106
7107 checkpoint48c_post (2003/02/06)
7108 Modifications in treatment of initial flux forcing controls
7109 to avoid extra storing of flux fields.
7110
7111 checkpoint48c_pre (2003/01/21)
7112 o Added tidal_basin_2d experiment (currently 1D!)
7113 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
7114
7115 checkpoint48b_post (2003/01/27)
7116 o r* coordinate added in #ifdef NONLIN_FRSURF block.
7117 (modification to pressure gradient not yet implemented)
7118 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
7119 (for U & V) that are used for vertical advection of momentum.
7120
7121 checkpoint48a_post (2003/01/24)
7122 o In preparation for r*, use temp. array to compute vertical transport
7123 in flux-form momentum pkg. => change results of few test-exp.
7124 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
7125 lab_sea, natl_box & plume_on_slope
7126
7127 checkpoint48 (2003/01/23)
7128 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
7129
7130 checkpoint47j_post (2003/01/21)
7131 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
7132 o moved adexch from forward_step to addummy_in_stepping
7133 o added exch in ctrl_map_...
7134 o aveFreq.=0. at end of cost_final to avoid overwrite in
7135 reverse checkpointing loop
7136 o Yet more changes in gmredi:
7137 * adgmredi_calc_tensor
7138 avoiding all recomputation of gmredi_slope_limit
7139 * adgmredi_x/y/rtransport
7140 added flag for excessive storing to avoid recomp. of
7141 u/v/rtans, dTdx/y/z
7142 -> this is not really necessary and very memory-consuming
7143 * adgmredi_slope_psi:
7144 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
7145 * gmredi_slope_limit
7146 re-activated full calculation of taperfct for case 'ac02'
7147 o updating verification/ adjoints of carbon, global_ocean.90x40x15
7148
7149 checkpoint47i_post (2003/01/13)
7150 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
7151 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
7152 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
7153 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
7154 o gmredi: fix few bugs.
7155
7156 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
7157 This will be a good checkpoint to plug into the ecco-branch.
7158 o few modif.'s to get latest version adjointed
7159 (mainly kick out code in ini_linear_phisurf)
7160 o modif's to run adjoint with exactConserv
7161 o case GM_BOLUS_ADVEC should be cleaned
7162 S/R gmredi_slope_psi should be cleaned
7163 o verification/carbon now has exactConserv=.TRUE.
7164
7165 checkpoint47g_post (2003/01/10)
7166 o time-average AIM output: becomes independent from statvars time-average
7167 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
7168 o After TAF bug fix:
7169 Tested adjoint of gmredi package.
7170 Tests were done with checkpoint47 rather than with latest
7171 checkpoint47f_post since the latter is broken for the adjoint
7172 verification/carbon/ contains both ADM and TLM gradient checks.
7173 Here they are, before they get changed/lost/stolen.
7174 Mostly modif.'s to fix numerical sensitivities.
7175 Gradient checks OK for
7176 - GM_taper_scheme:
7177 * clipping
7178 * ac02
7179 * linear
7180 * glw91
7181 * dm95
7182 * ldd97
7183 - GMREDI_OPTIONS:
7184 * GM_VISBECK_VARIABLE_K
7185 * GM_NON_UNITY_DIAGONAL
7186 * GM_EXTRA_DIAGONAL
7187 * GM_BOLUS_ADVEC
7188 in conjunction with data.gmredi parameters to be checked in
7189 in a few minutes under verification/carbon/code/
7190
7191 checkpoint47f_post (2002/12/28)
7192 Merging from release1_p10:
7193 o modifications for using pkg/exf with pkg/seaice
7194 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
7195 and SEAICE_EXTERNAL_FLUXES
7196 - pkg/exf CPP options EXF_READ_EVAP and
7197 EXF_NO_BULK_COMPUTATIONS
7198 - usage examples are Experiments 8 and 9 in
7199 verification/lab_sea/README
7200 - verification/lab_sea default experiment now uses
7201 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
7202
7203 checkpoint47e_post (2002/12/27)
7204 o created a tag prior to creating a branch
7205
7206 checkpoint47d_post (2002/12/16)
7207 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
7208 at the bottom boundary had an erroneous half slip boundary condition
7209 o added bottom drag and no slip boundary condition capabilities to
7210 oceanic pressure coordinates code
7211 o added new verification experiment global_ocean_pressure, this experiment is
7212 also described in the tutorial section of the manual
7213 checkpoint47d_pre (2002/12/16)
7214
7215 checkpoint47c_post (2002/12/16)
7216 o Added a verification experiment for a global cubed-sphere ocean run
7217 - verification/global_ocean.cubed32x32x30
7218 - uses pkg/therm_seaice and pkg/bulk_forcing
7219
7220 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
7221 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
7222 when using P-coordinate; only implemented for atmospheric config.
7223 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
7224 NOTES: requires option NONLIN_FRSURF to be "#define".
7225 o update advect_xz/results/output.txt (left from checkpoint44g_post)
7226
7227 checkpoint47b_post (2002/12/05)
7228 Merging from release1_p9:
7229 o pkg/seaice
7230 - removed GOTO's and added taf directives
7231 - double precision constants to reduce the g77 (Linux)
7232 to F77 (SGI) differences reported in release1_p8
7233 o tools/genmake
7234 - added SGI options
7235 o verification/testscript
7236 - updated to that of checkpoint47a_post
7237 o verification/global_ocean.90x40x15/input/eedata
7238 - modified for SGI f77 compatibility
7239 o verification/lab_sea
7240 - added description of sea-ice model
7241 - added missing matlab routines
7242 - added test of thermodynamics parallelization
7243
7244 checkpoint47a_post (2002/11/23)
7245 o new pkg: aim_v23
7246 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
7247 for now, keep the same surface forcing as before.
7248 - Part-Cell implemented into AIM; check that Heat & Water are conserved
7249 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
7250 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
7251 o add diagnostic of surface correction term in monitor output
7252
7253 o bulk_force and therm_seaice
7254 - Two packages: bulk_force (Bulk forcing)
7255 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
7256 - Earlier integration from Stephaine Dutkiewicz
7257 and Patrick Heimbach.
7258 - Two ifdef statements for compile time,
7259 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
7260
7261 checkpoint47 (2002/11/15)
7262 differentiable version of checkpoint46n_post
7263 o bug fix in quasihydrostaticterms
7264 o * "clean" adjoint code (in terms of extensive recomputations)
7265 can now be obtained for all GMREDI options (i.e. for
7266 - GM_VISBECK_VARIABLE_K
7267 - GM_NON_UNITY_DIAGONAL
7268 - GM_EXTRA_DIAGONAL
7269 - GM_BOLUS_ADVEC )
7270 * However, wrong gradient check problem remains unsolved.
7271 * New CPP options have been introduced for different
7272 tapering schemes
7273 o external_fields_load now part of differentiation list
7274 o pressure needs multiple storing;
7275 would be nice to have store_pressure at beginning or
7276 end of forward_step, e.g. by having phiHyd global (5-dim.)
7277 (NB: pressure is needed for certain cases in find_rho,
7278 which is also invoked through convective_adjustment).
7279 o recomputations in find_rho for cases
7280 'JMD95'/'UNESCO' or 'MDJWF' are OK.
7281 o #define ATMOSPHERIC_LOADING should be differentiable
7282 o ini_forcing shifted to begining of initialise_varia
7283 o Incorporating QNVS line search routines into MITgcm
7284 (this is separate code, and therefore not under pkg)
7285 lsopt/, optim/
7286 o Updated verification/carbon/
7287 - #define GM_VISBECK_VARIABLE_K
7288 - GM_taper_scheme = 'ldd97'
7289
7290 checkpoint46n_post (2002/11/12)
7291 Merging from release1_p8:
7292 o verification/natl_box:
7293 updating new external_fields_load routine
7294 o New package: pkg/seaice
7295 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
7296 The sea-ice code is based on Hibler (1979-1980).
7297 Two sea-ice dynamic solvers, ADI and LSR, are included.
7298 In addition to computing prognostic sea-ice variables and diagnosing
7299 the forcing/external data fields that drive the ocean model,
7300 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
7301 The implied surface heat flux is then stored in variable
7302 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
7303 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
7304 non-local transport term. Because this call precedes model
7305 thermodynamics, temperature under sea-ice may not be "exactly" at
7306 the freezing point by the time theta is dumped or time-averaged.
7307 N.B.: fairly large differences in accuracy occur across
7308 different platforms/compilers; comparison between
7309 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
7310 generated output gives:
7311 T S U V
7312 C D M c m s m s m s m s
7313 n p a R g m m e . m m e . m m e . m m e .
7314 f n k u 2 i a a d i a a d i a a d i a a d
7315 g d e n d n x n . n x n . n x n . n x n .
7316
7317 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
7318 o GAD:
7319 - generated new common blocks to account for call of
7320 same gad routines with differing traceridentities
7321 (needed to modify tracerIdentity indices in GAD.h)
7322 - generated separate common blocks for case useCubedSphereExchange
7323 (Department of Futurology)
7324 - parameter lists to gmredi_?transport: added tracerIdentity
7325 - added new key indices to tamc.h
7326 o external_fields_load:
7327 - added this routine to TAF list
7328 - needed to make some common blocks global and additional storing
7329 along the same lines as exf package (checkpoint_lev?_directives.h)
7330 o exf:
7331 updated external forcing package
7332 - bug fixes carried over from ecco-branch
7333 (missing OBCS_OPTIONS.h in two routines)
7334 - enable easy to use "no forcing".
7335 - added exf I/O for atmospheric loading
7336 - added exf I/O for runoff data
7337 - transfered scaling between exf <-> MITgcm to exf namelist
7338 o Adding new verification experiment global_with_exf.
7339 This verification experiment is almost identical to the
7340 global_ocean.90x40x15 experiment, except that it uses
7341 the exf (and cal) package instead of the
7342 external_fields_load routine (cf README file).
7343
7344 checkpoint46m_post (2002/11/07)
7345 o modified testscript to return -- when there are no lines of "%MON" output
7346 o added new flag "quasiHydrostatic" for QH mode
7347 and new routine quasihydrostaticterms()
7348 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
7349 New routine: mom_u_coriolis_nh()
7350 o fixed sign of non-hydrostatic metric terms in u and v equations.
7351 Depend on correct sign of gravitySign.
7352 o added work.pc* to .cvsignore in aim directories using ifc
7353 o introduced flag for controllin non-hydrostatic metric terms
7354 o removed gravitySign from PARM04
7355 o switched to g77/ifc from pgf77 in aim experiments
7356
7357 checkpoint46l_post (2002/11/01)
7358 o made convective adjustment work with pressure coordinates:
7359 - changed the direction of k-loop in convective_adjustment.F for the
7360 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
7361 - adjusted the reference pressure k-index in convective_adjustment.F
7362 - adjusted the convection condition in convect.F (in analogy to
7363 calc_ivdc.F)
7364 - convective_adjustment no longer computes anything on the halos
7365 - removed the warnings about negative salinity from find_rho.F and
7366 find_alpha.F; instead the new routine look_for_neg_salinity, called
7367 at the beginning of find_rho, find_alpha, and find_beta, does a
7368 check of the entire slice, if CPP-option
7369 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
7370 checkpoint46l_pre (2002/10/23)
7371
7372 checkpoint46k_post (2002/10/23)
7373 o fixed the verification/global_ocean.90x40x15 experiment:
7374 - new bathymetry (the world according to A., JMC, and M.)
7375 - new initial fields and forcing fields (*.bin files)
7376 - new POLY3.COEFFS (for the next release one should switch to a full
7377 equation of state: JMD95P or MDJWF)
7378 - fixed several errors and redundancies in the data file
7379 - experiment uses looped cells
7380 - added matlab directory with diagnostic scripts for plotting of output
7381
7382 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
7383 - read AIM physics parameters from a file (data.aimphys)
7384 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
7385
7386 checkpoint46j_post (2002/10/07)
7387 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
7388 o move wVel computation at the end of the time step, in S/R integr_continuity
7389 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
7390 o update timeave pkg for wVel diagnostic.
7391 checkpoint46j_pre (2002/09/27)
7392
7393 checkpoint46i_post (2002/09/25)
7394 o Clean up AIM package (and keep the results unchanged):
7395 include CPP_OPTION and use IMPLICT NONE in all routines ;
7396 declare all the variables _RL ; use _d 0 for all numerical constants.
7397 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
7398
7399 checkpoint46h_post (2002/09/25)
7400 o cleaned up the use of rhoNil and rhoConst.
7401 - rhoNil should only appear in the LINEAR equation of state, everywhere
7402 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
7403 and the dynamical equations are all divided by rhoConst
7404 o introduced new parameter rhoConstFresh, a reference density of fresh
7405 water, to remove the fresh water flux's dependence on rhoNil. The default
7406 value is 999.8 kg/m^3
7407 o cleanup up external_forcing.F and external_forcing_surf.F
7408 - can now be used by both OCEANIC and OCEANICP
7409 checkpoint46h_pre (2002/09/18)
7410
7411 Added code to convert surface volume flux (fresh water) into
7412 a mass flux when using P coordinates in the ocean (OCEANICP).
7413 Note: It assumes you have set rho0=rhoConst=density of fresh water.
7414
7415 checkpoint46g_post (2002/09/18)
7416 o Include a new diagnostic variable phiHydLow for the ocean model
7417 - in z-coordinates, it is the bottom pressure anomaly
7418 - in p-coordinates, it is the sea surface elevation
7419 - in both cases, these variable have global drift, reflecting the mass
7420 drift in z-coordinates and the volume drift in p-coordinates
7421 - included time averaging for phiHydLow, be aware of the drift!
7422 o depth-dependent computation of Bo_surf for pressure coordinates
7423 in the ocean (buoyancyRelation='OCEANICP')
7424 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
7425 Theta, Salinity, and Pressure in the parameter list. This routine is
7426 presently contained in find_rho.F. This routine does not give the
7427 correct density for 'POLY3', which would be a z-dependent reference
7428 density.
7429 o cleaned up find_rho
7430 - removed obsolete 'eqn' from the parameter list.
7431 o added two new verification experiments: gop and goz
7432 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
7433 checkpoint46g_pre (2002/09/16)
7434
7435 checkpoint46f_post (2002/09/16)
7436 o Enable tangent linear (forward mode) gradient checks:
7437 - extended active file handling to g_... files
7438 - added TANGENT_SIMULATION to theSimulationMode
7439 - extended grdchk package accordingly
7440 o added tangent linear setup in verification/carbon/code_ftl
7441 o added adjoint setup in verification/front_relax/code_ad
7442
7443 checkpoint46e_post (2002/09/05)
7444 o Added new equation of state -> MDJWF
7445 - EOS of McDougall et al., 2002, JAOT, submitted
7446 - caveat: the equation of state is only valid for a smaller (more
7447 realistic?) range of values than JMD95P/Z and UNESCO
7448 - added masks to the calculation of pressure in store_pressure
7449 - added more check values for density in check_eos (ini_eos.F), some of
7450 the old check values are out of the range of the MDJWF-eos, so don't
7451 expect perfect matches for those
7452 checkpoint46e_pre (2002/08/19)
7453
7454 checkpoint46d_post (2002/08/19)
7455 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
7456 'OCEANICP', also initialised field pressure correctly in ini_eos in the
7457 case of pressure coordinates. eosType='JMD95Z' in
7458 combination with buoyancyRelation='OCEANICP' now causes an error.
7459 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7460 in find_alpha/beta.
7461 checkpoint46d_pre (2002/08/15)
7462
7463 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7464 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
7465
7466 checkpoint46c_post (2002/08/15)
7467 o Changes necessary for ocean in p-coordinates
7468 - Added new buoyancy relation = 'OCEANICP'
7469 - Added new parameters = gravitySign (this used to be contained inside
7470 the factor dRdZ which I added when we first switched to R coordinates).
7471 X GM/Redi is not compatible (yet)
7472 X bottom drag and no-slip need to be debugged.
7473 checkpoint46c_pre (2002/08/07)
7474
7475 checkpoint46b_post (2002/08/07)
7476 o Added new equation of state -> JMD95Z and JMD95P
7477 - EOS of Jackett and McDougall, 1995, JAOT
7478 - moved all EOS parameters into EOS.h
7479 - new routines ini_eos.F, store_pressure.F
7480 o Added UNESCO EOS, but not recommended because it requires
7481 in-situ temperature (see JMD95)
7482 o Modified formatting for knudsen2.f in utils/knudsen2 and added
7483 unesco.f to be used with POLY3
7484 checkpoint46b_pre (2002/07/31)
7485
7486 checkpoint46a_post (2002/07/31)
7487 o Added (atmospheric) pressure loading
7488 - new field in FFIELDS.h, etc...
7489 - new cpp flag ATMOSPHERIC_LOADING
7490 o Changed hFacC to _hFacC in calc_phi_hyd.F
7491 o Added SHORTWAVE_HEATING to some files for consistency
7492 checkpoint46a_pre (2002/07/13)
7493
7494 checkpoint46 (2002/07/13)
7495 further merges from release1_p5
7496 o new ctrl package
7497 - adopted from ECCO environment to enable optimization
7498 - added Eliassen Palm fluxes to controls
7499 o added Eliassen Palm flux controls to gradient check package
7500 o cost package
7501 - Compatible with new ctrl package
7502 - added Eliassen Palm cost hooks
7503 - modif's of existing cost functions
7504 o Adjoint-related bug fixes in kpp:
7505 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
7506 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
7507 o autodiff package
7508 - flow directives:
7509 + new for S/R do_the_model_io
7510 + enhanced for S/R checkpoint
7511 + new gmredi.flow
7512 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
7513 disable adcommon.h/g_common.h by default.
7514 - fixed problem for adjoint of global_max
7515 o modified verification/carbon/
7516 o New setup for adjoint of global_ocean
7517 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
7518 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
7519 o incorporated hooks for sponge layer code (external_forcing.F)
7520
7521 checkpoint45d_post (2002/07/12)
7522 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
7523 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
7524 (affects plume_on_slope "cg2d" output)
7525 o add new parameter deltaTfreesurf for free-surface time stepping
7526 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
7527 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
7528 o change phiMin in exp1 (to agree with documentation)
7529 o add new flags:
7530 - T,S forcing inside/outside Adams-Bashforth
7531 - turn off temp,salt advection and/or forcing
7532 - for each tracer, define internal flag for multiDimAdvection & A-B
7533 o monitor: change definition of KE to check conservation of Energy
7534
7535 checkpoint45c_post (2002/05/30)
7536 o Removed f90 comments ("!")
7537 o Modified initialisations to enable exf package for MITgcm
7538 (without invoking ECCO_PACKAGE).
7539 o modifications to gradient check package (Martin Losch)
7540 - enable centered differences
7541 - modified format of standard output
7542
7543 checkpoint45b_post (2002/05/30)
7544 o cleaned exchange calls in cg2d
7545 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
7546 o included CPP option SINGLE_LAYER_MODE in thermodynamics
7547 to configure barotropic setup (Martin Losch)
7548 o moved some initialisations within bi,bj loop in dynamics
7549 (TAF flow dependency)
7550 o in initialise_varia, moved call packages_init_variables
7551 before convective_adjustment_init
7552 (corresponding adjustment of TAF tape initialisation).
7553 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
7554
7555 checkpoint45a_post (2002/05/01)
7556 o compute Rho over the whole domain (extend iMin,jMin indices)
7557 o specific exchange for X-slice domain (case Ny=1)
7558 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
7559 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
7560
7561 checkpoint44h_post = checkpoint45
7562 o Fix to restore differentiability:
7563 place at which packages_init_variables is called in
7564 initialise_varia is crucial for reverse control flow.
7565 o modifications in GMRedi to enable stable adjoint
7566 (corresponding modif's in thermodynamics, dynamics)
7567 o added missing hook for sponge layer code in external_forcing
7568 o modified test cost functions
7569 o storing in gad_advection (plus removal of write(0,*)!
7570 o missing headers TR1.h added in convective_adjustment routines
7571 o errorMessageUnit set non-equal zero in eeboot
7572 (conflict on some platforms, e.g. IBM SP3)
7573 o modified carbon verif.
7574
7575 checkpoint44h_pre (2002/03/14)
7576 o vertical grid option: allow to put the Interface at the middle between
7577 2 cell-centers ; replace delZ in pkg/kpp by drF.
7578 o GM Advective form: Tracers are advected using the residual transport (=
7579 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
7580
7581 checkpoint44g_post (2002/03/05)
7582 o fix surface correction term in multiDimAdvection (affects plume_on_slope
7583 results) ; ifdef missing in thermodynamics.F
7584
7585 checkpoint44f_pre,checkpoint44f_post
7586 o added PTRACERS package
7587 This allows an arbitrary number of passive tracers to be integrated
7588 forward simultaneously with the dynamicaly model.
7589 + Implemented so far:
7590 - basic forward algorithm (time-stepping, advection, diffusion, convection)
7591 - I/O and checkpointing
7592 - GM/Redi *but* using the GM/Redi coefficient of Salt
7593 + Not implemented so far:
7594 - KPP
7595 - OBCS
7596 + No specific example supplied (yet) but global_ocean.90x40x15 has the
7597 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
7598 line in data.pkg.
7599 + This package is disabled by default since it increases storage.
7600
7601
7602 o testscript: added -cleanup option
7603 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
7604 b) enable to filter 2D fields.
7605
7606 checkpoint44e_pre,post
7607 o re-wrote convective adjustment to use pre-calculated weights
7608 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
7609 Adds: model/src/convective_weights.F, convectively_mixtracer.F
7610 Original calls to convect() still in place.
7611
7612 chkpt44d_pre,post
7613 o added missing EXCLUDE_MONITOR flags
7614 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
7615 (incompatible typ in MIN/MAX expressions caused problems
7616 on IBM SP3)
7617 o in genmake added variable MAKEDEPEND
7618 plus resetting for case SunOS
7619 o added timer_stats.c routine for IBM SP3
7620 o removed variables in dynamics
7621 !!! I forgot to create tag chkpt44d_pre !!!
7622 !!! But chkpt44d_pre = chkpt44c_post !!!
7623
7624 o real fresh water flux implemented with non-linear free-surface.
7625
7626 chkpt44c_pre,post
7627 o few fix (mask in shap_s2, EmPmR in external_field_load,
7628 USE_NATURAL_BCS in solve_for_P);
7629 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
7630
7631 checkpoint44b_pre/_post
7632 o merge of relevant stuff from the ecco-branch:
7633 - genmake: removed $S64 overwrite for case SunOS
7634 - pkg/exf: update and corrections for field swapping and obcs
7635 - pkg/ecco: parameter lists for the_model_main, the_main_loop
7636 harmonized between ECCO and MITgcm
7637 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
7638 updated checkpointing_lev... lists for obcs
7639 - model/src: minor changes in forward_step, plot_field
7640 added directive for divided adjoint in the_main_loop
7641 - pkg/mdsio: added mdsio_gl_slice
7642
7643 o check parameters & config (chkpt44a_pre,post)
7644 o OBC and NonLin_FrSurf.
7645
7646 checkpoint44 (2002/01/18)
7647 o fix bug in mom_vi_del2uv
7648 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
7649 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
7650 o update AIM experiments (NCEP input files)
7651 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
7652 o added some stuff for AD
7653
7654 checkpoint43 (2001/09/28)
7655 o added two new advection tests
7656 o added global 4x4 degree ocean test
7657 o added test of H&S94 with free surface on cube
7658 o some final mods for gradient check, adjoint,...
7659
7660 checkpoint42 (2001/09/27)
7661 Fixed AD-related problems:
7662 o Store directives up-to-date with re-arranged Adams-Bashforth
7663 (mainly thermodynamics.F)
7664 o New store directives for multi-dim. advection schemes
7665 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
7666 * new common block and key passkey
7667 (mainly gad_advection.F)
7668 o Modified store directives for split of dynamics/thermodynamics
7669 for the case ALLOW_KPP
7670 o Cleaned argument list for timestep_tracer.F
7671
7672 checkpoint41 (2001/09/27)
7673 o re-formatted/added comments in prologues of key subroutines
7674 to work with protex
7675
7676 checkpoint40 (2001/09/27)
7677 o moved calc_gs, calc_gt and calc_tr1 back to model/src
7678 o added FLT (floats) package from Arne along with demo. experiment
7679 o re-arranged Adams-Bashforth scheme for tracers to allow easier
7680 implementation of forward-in-time forcing terms
7681 o more mods for non-linear free-surface including new variable
7682 o modified multi-dim method to work on cube
7683 o bug fix in KPP (from DM)
7684
7685 checkpoint40pre9 (2001/09/27)
7686 o added DST advection schemes
7687 o fix MPI bug on SGI's
7688 o modifications for non-linear free-surface
7689 o fixed conditionals for fixed flow/passive tracer only mode
7690 o added tension/strain form of stress tensor
7691 o changes to commenting of arguments for TAF/TAMC
7692 o added/updated many matlab scripts
7693 o added multi-dimensional advection method for tracers
7694
7695 checkpoint40pre8 (2001/09/05)
7696 o new package rw/
7697 Added method for dumping intermediate local arrays:
7698 mdsio_writetile - same as mdsio_writefield except works from inside
7699 bi,bj loop
7700 mdsio_writelocal - same as mdsio_writetile except works for local
7701 arrays
7702 write_local_r? - higher-level wrapper for mdsio_writelocal
7703 Controlled by diagFreq. Defaults to zero (ie. no dumps)
7704 Example given at end of mom_vecinv.F that dumps some local arrays.
7705 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
7706 control flux-form versus vector invariant code.
7707 Switch is runtime flag vectorInvariantMomentum (defaults to false)
7708 or genmake -DISABLE ...
7709 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
7710 (additional storing is now needed for case vecinv;
7711 currently nothing implemented to switch this storing off
7712 in case fluxform is used since no CPP flag available).
7713
7714 checkpoint40pre7 (2001/08/14)
7715 o bug fix in dynamics.F
7716 calc_viscosity called before k=1,Nr loop.
7717 o added some #ifdef's ALLOW_PASSIVE_TRACER
7718 o cleaned initialisations in ctrl_map_ini
7719 related to TAF
7720
7721 checkpoint40pre6 (2001/08/13)
7722 o split dynamics into thermodynamics & dynamics
7723 o corresponding split of calc_diffusivity into
7724 calc_diffusivity, calc_viscosity
7725 (kpp_calc_diff, kpp_calc_visc).
7726 o Added diffkr, kapgm to control variables
7727 o bug fix in gmredi_slope_limit for ldd97
7728
7729 checkpoint40pre5 (2001/07/31)
7730 o proper initialization of Adams-Bashforth time stepping
7731 + uses forward step for very first step of model (iter=0)
7732 o re-generated *all* output since almost all output is modified by this
7733 change (sorry but we've been putting this one off for about 2 years)
7734 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
7735 *not* regenerated since they are already out of date and I don't
7736 want to create the impression that they are suddenly working.
7737 o removed KAP stuff for DEC's
7738 o modified/added many .cvsignore files in */code and */input
7739 o added new expt "solid-body.cs-32x32x1"
7740 + this uses an alternative form of ini_curvilinear_grid.F which
7741 is not necessarily any better than the current one...
7742
7743 checkpoint40pre4 (2001/07/30)
7744 o added re-initialisations of utrans,vtrans,rtrans in
7745 calc_common_factors which are crucial for TAF.
7746 o extended iMin,jMin range for calc_common_factors,
7747 calc_diffusivity
7748 o added option ALLOW_PASSIVE_TRACER
7749 o a few minor updates and fixes
7750
7751 checkpoint40pre3 (2001/07/13)
7752 o created calc_gtr1.F for gad package
7753 o split the_main_loop and re-introduced forward_step
7754 o some recomputations of nIter0 for TAMC
7755
7756 checkpoint40pre2 (2001/07/13)
7757 o Updated to latest branch of AJA, JMC
7758 o Added gradient check package
7759 o Added routines for passive tracer handling
7760 o Added carbon sequestration sensitivity experiment
7761
7762 checkpoint39 (2001/05/14)
7763 o Modifications and fixes to support TAMC
7764 (mainly missing or wrong directives)
7765 o Corrected common blocks when fooling TAMC to produce adjoint I/O
7766 in addummy_in_stepping
7767 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
7768 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
7769 o Included following packages:
7770 cal: calendar
7771 exf: external forcing
7772 ecco: essential routines to control use of cal, exf
7773 (NB: this is not the full ECCO environment)
7774 o disabled some packages by default in genmake
7775
7776 checkpoint38 (2001/04/10)
7777 o see notes_c37_adj.txt
7778 o corrected wrong layer index in external_forcing_t
7779 o replaced the_main_loop/forward_step by the_main_loop
7780 o removed forceoutput from write_state
7781 (replaced criteria for initial/final state)
7782 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
7783
7784 checkpoint37 (2001/03/13)
7785 o mdsio.F routine split and packaged in pkg/mdsio
7786 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
7787 used unless genmake -disable=mdsio)
7788 o allow a more precise surface-geopotential gradient for the atmosphere
7789 taking into account the change in space of Alpha (=1/rho) at the surface.
7790 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
7791 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
7792 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
7793 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
7794 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
7795 o Time-Average diagnostics defined as a pseudo package "timeave".
7796 o pickup files : old pickup (before c35) did not work with new code (c35
7797 and after) unless activating 2 commented lines in initialise-varia.
7798 o Non-Hydrostatic pickup file Pb fixed.
7799 o bug with Rigid-lid version (since c35) fixed.
7800
7801 checkpoint36 (2001/02/20)
7802 o implement Crank-Nickelson barotropic time-stepping
7803 o recover Time-Average diagnostics
7804 o fix Pb in checkpoint (PR#19)
7805 o AIM become a standard package ; clean unused CPP_kees
7806
7807 checkpoint35 (2001/02/08)
7808 o subtantial rewrite of dynamics.f
7809 o allows staggered time-stepping
7810 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
7811 o added bottom drag (linear + quadratic)
7812
7813 checkpoint34 (2001/01/30)
7814 o Modified exchange routines for correct reverse simulation.
7815 o Added verification output to comply with bug fix in impldiff.F
7816 as of c33 (exp2, natl_box).
7817 o Corrected store directives in dynamics.F
7818 o Corrected array boundaries in impldiff.F
7819 o Corrected array dimensions in gmredi.
7820 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
7821 o Added routine GLOBAL_SUM_INT to global_sum.F
7822 o Added mdsio_gl.F for ECCO purposes.
7823
7824 checkpoint33 (2000/11/30)
7825 o Fixed bug in lower BC in impldiff.F
7826 o Fixed confusion about units of forcing arrays in FFIELDS.h
7827 namely Fu,Fv,Qnet,Qsw,EmPmR:
7828 - Removed verification/natl_box/code/external_fields_scale.F
7829 (did not differ from that in model/src)
7830 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
7831 (see FFIELDS.h for description)
7832 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
7833 kpp_calc.F and kpp_transport_t.F
7834 - Removed model/src/external_fields_scale.F and calls to it
7835 - verification/natl_box uses flux data with "atmospheric" sign so
7836 a special version of external_fields_load.F is used to
7837 change the data as it's read in. This way, the arrays
7838 have the right units and signs at all times tha a user could
7839 possibly use them.
7840 o Corrected genmake to delete a temporary file during configuration
7841
7842 checkpoint32 (2000/11/13)
7843 o Scaling of forcing fields moved from external_forcing.F to
7844 external_fields_scale.F, called directly after loading fields.
7845 o Surface relaxation terms added to surface tendency fields in
7846 extra subroutine.
7847 o impldiff.F changed to avoid storing by TAMC of huge intermediate
7848 fields.
7849 o Changes in GMRedi to comply with packaging structure.
7850 o Modifications and bug fixes in KPP package.
7851 o Verification experiment for KPP added (verification/nat_box/)
7852
7853 checkpoint31 (2000/09/11)
7854 o Packages interface brought in line with defined standard
7855 -> new routines packages_...F
7856 -> changes in initialise_fixed.F, initialise_varia.F
7857 -> enables initialisation interface for ECCO package
7858 o Rescaling of external forcing fields immediately after read
7859 (removed from external_forcing.F)
7860 -> new: surface_fields_scale.F
7861 -> affects ini_foorcing.F, external_fields_load.F
7862 o Computation of surface tendencies before tendency updates.
7863 -> new: external_forcing_surf.F
7864 o Change of variable names useGMRedi, useKPP, useECCO
7865 o Further changes in dynamics.F, impldiff.F for TAMC
7866 o Tested for experiments 0, 2, 4.
7867 - not yet tested for GMRedi.
7868 - not yet tested for KPP.
7869
7870 checkpoint30 (2000/07/13)
7871 o Updates for OBCs
7872 o New experiment for test OBCs (internal_wave)
7873 o New output.txt in verification/exp4/results/
7874 o Updates for KPP: calculation of viscosity corrected, new variables
7875 kpp_dumpFreq and kpp_taveFreq
7876 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
7877 and entry for T90 in genmake
7878
7879 checkpoint29 (2000/06/21)
7880 o packaged KPP and GM/Redi
7881
7882 checkpoint28 (2000/06/09)
7883 o Corrected initialization of hFacMin for difference vertical coordinates
7884 o Modified calculation of partial cell thickness to more robust algorithm
7885 o config_summary.F: replaced write_1D_... by write_0D_...
7886 read_write.F: added subroutines write_0D_...
7887 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
7888 included some initialisations required for TAMC.
7889 o routine calc_isoslopes: modified sqrt computation to make it
7890 differentiable for zero argument.
7891 o routines dynamics, impldiff:
7892 included store directives and tape key computations required for TAMC.
7893 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
7894
7895 checkpoint27 (2000/04/10)
7896 o fixed calc_isoslopes() to so that cancellation of terms in tensor
7897 formulation works properly with variable resolution.
7898 o restructured the calling tree between the_model_main() and dynamics()
7899 o split initialise() into initialise_fixed() and initialise_varia()
7900 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
7901 in new routine ini_psurf()
7902
7903 checkpoint26 (2000/04/05)
7904 o moved some #ifdef in optional routines to encompass everything
7905 except the argument declarations. This was using up some memory.
7906 o fixed macros like _ADT to work with both versions of Linux cpp
7907 o cleaned up some unused and uninitialized variables
7908 (helps when debugging with strict compile options)
7909 o split up CPP_EEOPTIONS.h into options and macros
7910 (macros are now in eesupp/inc/CPP_EEMACROS.h)
7911 o patch for 2 processor JAM mode
7912
7913 checkpoint25 (2000/03/15)
7914 o updates for OBCs and NH
7915 o dramatically reduced memory usage
7916 o added "JAM" routines for use on Artic network
7917 o parameterization of convection by implicit vertical diffusion
7918 o added a diagnostic of convective index
7919 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
7920 (this is was partly for OBCs and NH but also in anticipation of
7921 an explicit free-surface option)
7922 o initial state input files for U and V
7923
7924 checkpoint24 (1999/08/02)
7925 o Removed some spurious "REAL"s
7926 o Updated KPP to latest version from JPL
7927 o Added a COS(latitude) in horizontal viscosity
7928
7929 checkpoint23 (1999/05/26)
7930 o Added del^4 diffusion for salt and temperature
7931 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
7932
7933 checkpoint22 (1999/05/18)
7934 o Made many small changes: implicit none, format(i5), etc...
7935 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
7936
7937 checkpoint21 (1999/05/18)
7938 o Introduced new I/O package that supports direct-access records (mdsio.F)
7939 o Split-up mid-level I/O routines
7940 o Updated input data for experiments 0,1,2,4 and 5
7941 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
7942
7943 checkpoint20 (1999/03/22)
7944 o Tidied up open-boundaries some more
7945 o Added non-hydrostatic code
7946 o Fixed some input data
7947 o Modified MPI start-up to work in "coupled" context.
7948
7949 checkpoint19 (1998/12/15)
7950 o Tidied up directory structure for verification experiments.
7951 o Added new code for open boundaries.
7952 o Corrected advective terms near boundaries.
7953 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
7954 o Implemented free-slip/no-slip BCs and del^4 dissipation.
7955 o Split default parameters out of ini_parms.F into set_defaults.F.
7956
7957 checkpoint18 (1998/11/30)
7958 o Further changes for optional code generation with
7959 CPP - ugh!
7960
7961 checkpoint17 (1998/11/03)
7962 o Beginning to incorporating modularity
7963 for supporting atmos. and ocean configs.
7964 o Small changes for TAMC complinace
7965 o New ultra simple test case. Barotropic box
7966 configuration "exp0".
7967
7968 checkpoint16 (1998/10/28)
7969 o Minor changes to exchange routines to support
7970 accumulation in reverse mode. Adjoint of an
7971 assignment is an addition.
7972 o Changes to support compilation by TAMC (LR(1)
7973 syntax) and by g77 under Linux ( 72 character
7974 limit ).
7975
7976 checkpoint15 (1998/09/29)
7977 Rewrote exchange routines to allow
7978 o General tile <-> tile connectivity.
7979 o TAMC reverse mode flag ( is this really needed? )
7980 o Variable width overlap and exchange region widths.
7981 o Hooks for sharing data via DMA, Arctic, Memory Channel,
7982 shmput/shmget, VIA, SYSV shmem and every other cool
7983 communication method.
7984
7985 checkpoint14 (1998/09/09)
7986 Consistent isomorphism chages made. These allow dynamical core
7987 to support both pressure and meters as a vertical coordinate.
7988
7989 checkpoint13 (1998/07/17)
7990 Release which corrects global_max problem and a couple
7991 of KGM time-averaging diagnostic errors. Also contains
7992 a double-gyre experiment setup as well as the baseline
7993 4 degree global template. The double gyre template is
7994 organised to allow it to be applied automatically to
7995 the baseline configuration.
7996
7997 branch-point-rdot
7998 A few tidy-ups have been made bt the real point of this
7999 check-point (excuse the pun) is to allow a branch to be
8000 made for the purposes of adding the rDot alterations.
8001 I don't want to commit the rDot to the main-trunk until
8002 we've actually tested it...
8003
8004 checkpoint12 (1998/07/08)
8005 Tidy up and added generic genmake script (formerly
8006 configure script).
8007 Released to testers.
8008
8009 checkpoint11 (1998/07/02)
8010 Re-arranged initialise() and introduced ini_vertical_grid()
8011 and ini_masks_etc().
8012
8013 checkpoint10 (1998/07/01)
8014 Introduced the configure script.
8015 Separated out the diags package.
8016 Added template for writing time-averages of tile/intermediate quantities.
8017 Updated SIZE.h in exp2 and made the data big-endian.
8018
8019 checkpoint9 (1998/06/22)
8020 MPI fix. Filename changes (meta/data). salbin*y stuff.
8021 General tidy-up.
8022 SST.bin SSS.bin added to verification/exp2
8023
8024 checkpoint8 (1998/06/22)
8025 Inludes time-dependant forcing and time-averaging.
8026 Works at 4x4 and 2.8125x2.8125 global
8027
8028 checkpoint7-4degree-ref
8029 Branch from checkpoint7. Released for application to
8030 global modeling and general modeling - process studies, regional
8031 model etc..
8032 Configured for verification/exp2 - 4 degree global, two process.
8033
8034 checkpoint7 (1998/06/15)
8035 Created by cnh
8036 Simple 4 degree global simulation
8037 configuration.
8038 Includes climatological wind,
8039 hydrography, bathymetry etc
8040 Does not include Heat Flux and E-P
8041
8042 checkpoint6 (1998/06/08)
8043 Created by cnh
8044 merged checkpoint5 with CD and
8045 spherical polar code.
8046 Still some problems with GM Redi
8047 abd full topography.
8048
8049 checkpoint5 (1998/06/08)
8050 Created by AJA
8051 contains updates to GM Redi
8052 and reordered timestepping loop
8053 for Implicit Diffusion.
8054
8055 checkpoint4 (1998/05/30)
8056 Created by cnh
8057 Contains memory saving macros ( _rdxc etc..) for when
8058 grid variations are limited.
8059 Contains polynomial coeffs for EOS and knudsen program
8060 for generation.
8061
8062 checkpoint3 (1998/05/26)
8063 Created by cnh
8064 Added extra flags for runtime options
8065 Added this file
8066 Added implicit free-surface
8067 Added pre-conditioner
8068 Put compare01 into repository ( compare01/... )
8069 Put data and eedata into repository ( verification/exp1 )
8070
8071 checkpoint2
8072 Created by AJA
8073 Added GM/Redi
8074
8075 checkpoint1
8076 Created by AJA
8077 Restructured kloop in dynamics.F
8078 Added non-linear EOS
8079
8080 baseline
8081 Original checked in code

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