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

Contents of /MITgcm/doc/tag-index

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


Revision 1.1941 - (show annotations) (download)
Tue Nov 19 00:03:51 2013 UTC (10 years, 6 months ago) by jmc
Branch: MAIN
Changes since 1.1940: +16 -1 lines
document changes in pkg/gmredi (GM_AdvForm); useOldFreezing removed
 and OAD_support/cb2mGetModules.csh + code_oad/CPP_OPTIONS.h

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1940 2013/11/17 15:48:18 jmc Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 o tools/OAD_support and (verification/*/) code_oad:
8 - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
9 module conversion ; remove unneeded CPP_EEOPTIONS.h.
10 - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
11 version (closer to model/incCPP_OPTIONS.h).
12 o model/src:
13 - remove parameter "useOldFreezing" from PARAMS.h and push it to the
14 retired list of parameters (routine FREEZE has been replace by surface
15 freezing (10.yrs ago) and by pkg/frazil (interior freezing).
16 o pkg/gmredi:
17 - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
18 velocity (same scheme but affects machine truncation) for GM_AdvForm.
19 - update output of FWD experiments: front_relax.bvp,
20 global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
21
22 checkpoint64q (2013/11/17)
23 o verification:
24 - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
25 tutorial_global_oce_biogeo and global_ocean.90x40x15.
26 - generate new output (growth & melt) for seaice_itd experiment after
27 updating the input pickup_seaice files (previously wrong).
28 o pkg/cost:
29 - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
30 (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
31 o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
32 cannot be applied to var in common block).
33 o allows to get results independent of tile-per-proc setting (if using
34 slower GLOBAL_SUM_SEND_RECV option).
35 - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
36 thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
37 forward gradients: update output).
38 - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
39 S/R and, for most exp., also comment out GLOBAL_SUM_R8.
40 o pkg/mom_common:
41 - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
42 code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
43 viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
44 ensure that all field value that are used are set.
45 o tutorial_deep_convection (smag3d):
46 - add missing scaling in mom_calc_smag_3d.F;
47 - set smag3D_coeff in input.smag3d such that results do not change.
48 o pkg/dic:
49 - change dic_cost.F to compute cost on each tile first and then apply
50 GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
51 tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
52 - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
53 o eesupp/src & pkg/mdsio:
54 - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
55 (from pkg/mdsio) since they are no longer used for tape IO.
56 - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
57 (+ keep a copy in pkg/atm_ocn_coupler).
58 o verification/isomip:
59 - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
60 o tools/build_options:
61 - optfile linux_amd64_ifort11, fast (no ieee) case:
62 to get a working restart for all experiments, add "-fp-model source"
63 to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
64
65 checkpoint64p (2013/10/20)
66 o pkg/autodiff:
67 - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
68 criteria, return to simple (default) tape IO format.
69 o pkg/mdsio (+ eesupp/src):
70 - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
71 previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
72 - fix globalFile and singleCpuIO options using simpler global mapping.
73 - new pairs of scatter/gather vector S/R (one for each type, generated from
74 template) corresponding to simpler global mapping.
75 - adread_write.F: switch to new S/R (but leave old calls commented) and write
76 to globalFile when parameter globalFiles is set to True.
77 - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
78 o pkg/autodiff:
79 - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
80 with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
81 missing, just add a STOP if array type do not match.
82 o pkg/exf:
83 - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
84 rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
85 and rename array obsSIce to exf_iceFraction.
86 o tutorial_deep_convection:
87 - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
88 for now all in this exp. code dir.
89 - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
90 testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
91 o eesupp/src:
92 - added SINGLE_DISK_IO option because reading of parameter files on
93 very large number of processors did not work with existing set-up
94
95 checkpoint64o (2013/09/25)
96 o pkg/atm_phys & atm_compon_interf:
97 - allows for coupling of gray-atmosphere (atm_phys) with ocean.
98 o tools/build_options:
99 - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
100 & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
101 remove CPP setting (was identical to genmake2 default).
102 o pkg/gmredi & model/src: Some updating and work done on the residual model.
103 - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
104 - fixed up the calculation of the eddy stress and how it is added to the
105 external forcing via taueddy_external_forcing.F
106 - at the moment, it is very experimental and only works with the variable eddy
107 diffusivity calculated in gmredi_k3d.F
108 o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
109 lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
110 o testreport (& tools/do_tst_2+2):
111 - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
112 o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
113 - remove CPP='cpp -traditional -P' (this is genmake2 default)
114 - add switch (for big setups) to use 'medium' memory-model (but leave it
115 commented out for now). Note: needed with FC 19 to compile big setups.
116 o pkg/atm_compon_interf:
117 - regroup per field origin (model & pkgs) the coupling storage routines
118 (which accumalate in time each coupling field)
119 - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
120 update accordingly + simplify aim_do_physics.F
121
122 checkpoint64n (2013/08/26)
123 o pkg/bbl:
124 - update formulation to reduce dispersion of tracer properties in bbl
125 - replaced horizontal and vertical transport parameters with velocities
126 - changes results for verification/global_with_exf.yearly
127 o verification/halfpipe_streamice:
128 - change to matrix construction; update both Fwd & AD output.
129 o verification/tutorial_tracer_adjsens:
130 - OpenAD test: switch to vector-invariant momentum since fluxform with
131 rStar causes problems with OpenAD; update output.
132 o tools:
133 - genmake2: define a common prefix for all temp-file names ; move them
134 to local /tmp disk (but would be easy to move them back);
135 - xmakedepend: apply the same switch for temp-files.
136 o pkg/offline:
137 - changes for use with rStar (NLFS): assume that we continue to provide
138 UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
139 output files) and apply r* scaling at each time-step (function of the time
140 varying Eta field); use normal pickup files (needed for restart with NLFS).
141 o adjoint with OpenAD:
142 - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
143 package openad. This package has to be compiled for all runs with OpenAD
144 instead of specifying code_oad_all as a modification directory.
145 - link the fortran templates from tools/OAD_support to the build directory
146 for preprocessing to avoid conflicts between different setups compiled
147 simultaneously and simplify cleanup.
148 o pkg/exf:
149 - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
150 main model or other pkgs are exchanged in EXF_MAPFIELDS).
151 o model/src:
152 - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
153 (similar to do_fields_blocking_exchanges.F).
154 o tools/genmake2:
155 - remove TAF output src code just before calling staf (when not doing a fresh
156 built, will stop if things go wrong with staf).
157 - fix target "adobj" (left from TAF version-2 transition)
158 o pkg/diagnostics:
159 - add a parameter to track the status of pkg/diagnostics activation;
160 this replace/extend the use of logical param "settingDiags" (to check
161 when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
162 New S/R to print error message and stop when pkgStatus is not right.
163 - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
164
165 checkpoint64m (2013/08/13)
166 o model/inc:
167 - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
168 8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
169 o pkg/kpp & aim_v23:
170 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
171 o pkg/seaice:
172 - restore (last time on 2011/12/24) ability to compile pkg/seaice with
173 undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
174 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
175 o eesupp/src:
176 - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
177 in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
178 o switch to TAF version-2:
179 - add flow directives to "freeze" naming convention for ad-routines that
180 are used in I/O routines of adjoint state and associated common blocks
181 that are used in adcommon.h (backward compatible with version-1)
182 - update all ad-optfiles (in tools/adjoint_options + few local to some
183 verification exp) to switch to latest TAF version (currently 2.5.5);
184 merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
185 out except for diva).
186 - the major change with TAF version-2 is that both the differentiated
187 routines and the forward routines (new) are returned as part of the TAF
188 output source code. Update genmake2 accordingly.
189 - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
190 with version-2 when compared to TLM or FWD gradient); other experiments
191 output show minor changes (machine truncation level); update the few AD &
192 TLM output with 12 matching digits only (some prior to version-2 switch).
193
194 checkpoint64l (2013/08/05)
195 o model/src:
196 - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
197 - main_do_loop.F: no longer includes additional (AUTODIFF) header files
198 when using TAF but only if using OpenAD.
199 o pkg/mom_common+fluxform+vecinv:
200 - always set horiz. viscosity arrays to background value before calling
201 MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
202 only when using variable horiz. viscosity (useVariableVisc=T);
203 - simplify mom_vecinv.F (only 1 block for momViscosity).
204 o pkg/mom_common: variable horiz. viscosity in NH code
205 - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
206 from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
207 - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
208 useBiharmonicVisc & useVariableVisc.
209 - fix old bug (already in 1rst implementation of variable horizontal viscosity
210 in calc_gw.F, version 1.27, 2006/06/20):
211 horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
212 even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
213 - change background horiz viscosity in vertical momentum (gW) to always be
214 viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
215 any type of variable viscosity, e.g., viscAh/4Grid)
216 - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
217 viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing
218 horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
219 default viscAh,viscA4 is zero).
220 o model/src:
221 - extend length of drC & recip_drC from Nr to Nr+1.
222 o Divided Adjoint (DIVA) with MPI:
223 - genmake2: do not create local ./mpi_headers dir when no file to copy into.
224 - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
225 and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
226
227 checkpoint64k (2013/07/23)
228 o tools/OAD_support:
229 - avoid the need for file "oadtempflile" in insertTemplateDir.bash
230 and remove it from genmake2.
231 o tools/build_options:
232 - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
233 MPI_HEADER_FILES list (let genmake2 find the missing headers)
234 o verification/halfpipe_streamice:
235 - change to driving stress formulation; update both Fwd & AD output.
236 o tools/genmake2 and Divided Adjoint with MPI:
237 - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
238 - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
239 - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
240 Makefile, which is set by genmake2, and check which mpi-headers are needed.
241 Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
242 - update target "CLEAN" (to also remove ./mpi_headers/ dir).
243 o testreport:
244 - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
245 perform additional runs (number of additional runs is "add_DIVA_runs" taken
246 from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
247 o verification/lab_sea (AD test):
248 - change to test Divided Adjoint Run in this set-up (both standard AD test
249 and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
250 o pkg atm_ & ocn_compon_interf:
251 - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
252 staggerTimeStep implementation) and disable (retired) corresponding
253 parameter.
254 o pkg/offline:
255 - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
256 - add S/R OFFLINE_CHECK to print offline parameter summary
257 and stop if loading a file that is not used;
258 - enable to calculate GMRedi tensor, KPP mixing and convective index
259 when the corresponding file(s) is/are not specified (but pkg is used).
260 - comment out resetting of monitorFreq (to endTime) since it still useful
261 for monitoring CFL numbers and checking offline fields.
262 o OpenAD:
263 - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
264 smaller standard output) and generate new (smaller) output (on baudelaire
265 using gfortran with -ieee) for exp. tutorial_tracer_adjsens
266 o model/src:
267 - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
268 (where external_forcing_adjust was called) and change list of arguments;
269 - merge external_forcing_adjust.F into external_forcing_surf.F
270 - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
271 which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
272 previously in file "balance_relax.F", now removed); remove corresponding
273 arrays in FFIELDS.h.
274 - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
275 a hack for getting back surfaceForcingS (loaded from file) when using
276 ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
277 - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
278 (was getting only 11 digits for AD-grad, due to different truncation
279 error in AD code).
280
281 checkpoint64j (2013/07/04)
282 o pkg/offline:
283 - to enable the use of other features with pkg offline (e.g., obcs),
284 also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
285 - comment out "allowFreezing" (now active) in 2 offline testing exp.
286 o pkg/exf ALLOW_RUNOFTEMP
287 - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
288 - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
289 - changes verification/global_ocean.cs32x15/results/output.seaice.txt
290 o pkg/atm_phys:
291 - allows to add some damping on uVel,vVel (strength only function of k).
292 o verification, ad-tests:
293 - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
294 global_ocean_ebm and offline_exf_seaice.thsice.
295 o verification/halfpipe_streamice:
296 - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
297 flux input boundary conditions to be ignored; a fix for this bug changed
298 verification results for forward test.
299 - add adjoint test.
300 o pkg/ptracers:
301 - allow to restart without SOM pickup (resetting SOM to zero).
302 o pkg/gmredi:
303 - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
304 - It uses mixing length theory and suppression by steering level effects to
305 calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
306 to JPO, for more details).
307 - It also uses the diffusivity to calculate an eddy induced streamfunction
308 based on a PV closure (rather than a buoyancy closure as in GM).
309 - New files added to pkg/gmredi:
310 gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
311 induced overturning streamfunction (called from gmredi_calc_tensor)
312 gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
313 for use in gmredi_k3d
314 gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
315 the eddy diffusivity
316
317 checkpoint64i (2013/06/18)
318 o pkg/cheapaml:
319 - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
320 that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
321 with pkg/cheapaml.
322 o utils/python: add subpackage for cubed sphere function, first example is
323 simple cs.pcol to plot 2D fields on a map
324 o pkg/streamice:
325 - This is a new package in MITgcm, which solves dynamic equations for ice
326 sheets and ice streams
327 - At the moment it is independent of atmosphere/ocean dynamics, or any
328 other physical packages in MITgcm, even ShelfIce (although it is anticipat-
329 ed that this will change)
330 - There is a new verification exercise that tests it, halfpipe_streamice,
331 evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
332 rectangular embayment
333 - halfpipe_streamice is forward-only for now, will have TAF test soon
334 - for questions, email dgoldber@mit.edu
335 o pkg/thsice:
336 - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
337 of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
338 - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
339 call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
340 - allow precip from pkg/cheapaml to make snow over seaice.
341 o pkg/cfc:
342 - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
343 - remove atmos CFC 2-D arrays from common bloc (now local variables)
344 - change some hard-coded constant to run time parameter for reading and
345 and interpolating atmospheric CFC ; keep same default as previously.
346 - more flexible reading of Atmos CFC (number of records no longer hard-coded)
347 - put arguments in standard order: myTime, myIter, myThid
348 - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
349 atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
350 - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
351 - new routine to print summary of CFC params and check for consistency.
352 o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
353 similar to thsice_advdiff.
354 Note that for the B-grid case the routine parameters uc/vc are overwritten.
355 o pkg/cfc:
356 - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
357 update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
358 - fix interpolation of atmphspheric CFC between Sorthern and Northern
359 hemisphere value.
360 o pkg/seaice:
361 - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
362 o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
363 so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
364 - requires an additional time level that is stored in the pickup
365 - you can start with AB2 from a pickup without this time level with
366 pickupStrictlyMatch = .false.
367
368 checkpoint64h (2013/05/26)
369 o pkg/cheapaml:
370 - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
371 affect machine truncation (but exp cheapAML_box still pass with 13 digits).
372 - consistent treatment of uWind,vWind location: assume everywhere in
373 pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
374 (Note: was already the case for Tair,Qair advection);
375 add option (INCONSISTENT_WIND_LOCATION) to recover old results.
376 - compute diabatic forcing only in the interior (excluding overlap regions)
377 - fill in array "Qsw" (for short-wave heating);
378 - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
379 before any update (consistent with MITgcm state var diagnostics);
380 - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
381 non periodic ; + adjusted for uWind,vWind (C-grid).
382 o pkg/seaice:
383 - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
384 add explicitly pkg/exf in experiments that currently use pkg/seaice.
385 - allows to compile pkg/seaice without pkg/exf.
386 o tools/OAD_support:
387 - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
388 of array "ourStepOf" in function rvNextAction (revolve.F90).
389 o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
390 - change pkg name (to be used with other atmospheric physics pkg)
391 but by-pass CVS when making the new pkg so that we keep the CVS history.
392 o pkg/offline:
393 - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
394 (previously called from pkg/dic_surfforcing_init.F)
395 o model/src:
396 - re-order sequence of calls within packages_init_variables.F, using
397 standard order, except for:
398 DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
399 CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
400 o new pkg: atm_phys
401 - add entry point and source code (previously in contrib
402 verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
403 (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
404 - re-order sequence of calls within packages_readparms.F,
405 packages_init_fixed.F and packages_write_pickup.F
406 (but skip packages_init_variables.F because of TAF issues).
407 - update contrib/*/atm_gray/ experiment.
408 o pkg/seaice (ITD code):
409 - simplify and fix the writing of pickup-files for ITD case
410 o pkg/seaice (ITD code):
411 - introduce floe size dependent lateral melt for ITD case;
412 - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
413 - update seaice_itd experiment main output.
414 o pkg/thsice:
415 - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
416 declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
417 changed accordingly pkg/atm2d.
418
419 checkpoint64g (2013/05/01)
420 o pkg/exf ALLOW_RUNOFTEMP
421 - if defined, river and glacier runoff temperature can be read-in from
422 runoftempfile; runoftempfile needs to have same format as runofffile
423 o pkg/thsice (& pkg/bulk_force):
424 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
425 for energy content of Precip + RunOff & Evap (like with pkg/exf).
426 - change computation domain to always be the interior (without overlap).
427 - fix bug (wrong overlap) when using EXF and stressReduction > 0.
428 o verification/tutorial_global_oce_biogeo:
429 - add preliminary OpenAD setup (still has problems)
430 o pkg/seaice:
431 - turn some parameters for choosing the convergence criterion of
432 the inexact Newton method (JFNK) into runtime parameters for convenience
433 - clean up seaice_calc_viscosities.F: remove/retire two options for
434 SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
435 the results of lab_sea/input because a division has been replaced by
436 a multiplication with the reciprocal (sumNorm)
437 - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
438 convergence of solver (changes results, of course), and to test some
439 new features
440 o model/src:
441 - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
442 - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
443 - move forcing adjustment (balancing surface forcing) in specific S/R
444 where might also be applied exchanges (if needed) to forcing arrays.
445 o pkg/shelfice:
446 - allow to specify the Ice-Shelf mass per unit area (instead of
447 shelficeLoadAnomaly) and do the conversion from one to the other
448 - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
449 to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
450 (b) will be loaded in time (before calling INI_PRESSURE) in case it is
451 needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
452 - update isomip experiment forward output (get machine truncation error
453 from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
454 o verification/offline_exf_seaice:
455 revise data.seaice in input.thermo and input_ad and update results accordingly
456 HO = 0.2, SEAICE_areaLossFormula = 2,
457 SEAICE_growMeltByConv = .TRUE.,
458 SEAICE_doOpenWaterMelt = .TRUE.,
459 Improve consistency with input.thsice and fix the spurious 500m ice corners
460 o verification/global_ocean.cs32x15:
461 - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
462 in icedyn (thsice+seaice-dyn) test and update output.
463 o verification/offline_exf_seaice:
464 - adjust list of tested variables (with testreport) and update
465 standard test output with better slection of monitored fields.
466 o pkg/cd_code:
467 - swtich off Adams-Bashforth on the 1rst iteration. Update output of
468 experiment lab_sea.hb87
469 o tools/genmake2:
470 - change default makedepend from the system default to tools/xmakedepend:
471 When no makedepend is specified, select tools/xmakedepend it the test pass,
472 otherwise select the system default (if exist and pass the test) or
473 try to build cyrus-makedepend ; stop if none of the 3 works.
474 o pkg/exf & pkg/thsice:
475 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
476 for energy content of Precip + RunOff & Evap. Assumes:
477 1) Rain has same temp as Air.
478 2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
479 3) Run-Off comes at the temp of surface water (with same Cp)
480 4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
481 put directly into Latent Heat flux & should use water-vapor heat capacity.
482 5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
483 with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
484 o pkg/seaice: simplify the use of CPP flags in JFNK-related files
485 (compile when SEAICE_ALLOW_JFNK is defined)
486 o pkg/thsice:
487 - fix oceanic flux diagnostics & timeave (left from new sequence of calls
488 implementation): move THSICE_AVE call after the advection (called directly
489 from thsice_do_advect.F).
490 o verification/global_ocean.90x40x15 and OpenAD:
491 New experiment for OpenAD is identical to the one in input_ad except that
492 multiDimAdvection=.FALSE.,
493 There is still an issue with this.
494 o pkg/thsice:
495 - account for ice velocity (ocean relative velocity) in turbulent heat flux
496 at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
497 and offline_exf_seaice (main test).
498
499 checkpoint64f (2013/03/31)
500 o verification/OpenAD:
501 - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
502 o verification/isomip, pkg/shelfice and OpenAD:
503 - add OpenAD setup to this exp and make shelfice package work with OpenAD
504 o verification/tutorial_global_oce_biogeo:
505 - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
506 o verification/offline_exf_seaice:
507 - replace adjoint experiment (now similar to fwd input.thermo/ setup).
508 o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
509 - add OpenAD setup to this exp and make ptracers package work with OpenAD
510 o pkg/seaice/seaice_evp.F:
511 mask the asymmetric contribution of the ice-ocean stress (when
512 the turningAngle is non-zero) over open water to avoid stripes
513 in the EVP-solutions after many EVP-substeps. This does not change
514 the verification experiment (because turningAngle=0 in that experiment),
515 but will affect other EVP solutions with turningAngle.ne.0
516 o verification, AD & TLM output:
517 - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
518 additions and multiplications which affect results at machine truncation
519 level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
520 lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
521 (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
522 digits of matching.
523 o pkg/seaice:
524 modify lsr-algorithm so that it vectorizes AND converges by using a
525 "zebra" method: split vector loop into two with step size 2; this
526 solves a general convergence problem for the JFNK solver on a vector
527 computer. It has the potential to even improve convergence for
528 non-vector machines, but it does change the results so it is turned
529 off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
530 SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
531
532 checkpoint64e (2013/03/05)
533 o pkg/ecco and several verification experiments:
534 Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
535 from ecco package, and revert to unified routine in model/src/
536 Adjust verification experiments accordingly, especially gloal_oce_llc90
537 Should conclude long-standing work by Gael to reconsile the_main_loop with
538 ECCO and will enable OpenAD's revolve loop in ECCO setup.
539 o pkg/generic_advdiff:
540 - implement compressible flow method for multi-dim advection (similar to
541 gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
542 TAF generates many recomputations) to use it; no yet coded with implicit
543 vertical advection.
544 - change experiment advect_cs (new output) and advect_xy (same output)
545 to test compressible flow multi-dim advection.
546 o pkg/generic_advdiff:
547 - fix SOM advection for unusual cases (linear Free-Surf in r*, other
548 cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
549 o pkg/seaice:
550 - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
551 bug affects two verification experiments (lab_sea and lab_sea.hb87),
552 recover old (wrong) results by setting noSlipFac = 2. in
553 seaice_calc_strainrates.F;
554 - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
555 - add runtime parameter SEAICE_JFNKepsilon for that finite difference
556 gradient in the Jacobian times vector operation (s/r seaice_jacvec)
557 - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
558 o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
559 - new subroutines seaice_lsr_tridiagu/v
560 - introduce loop bounds i/jmin/max to be able to use a restricted
561 additive Schwarz method, but not used for now.
562 - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
563 - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
564 o OpenAD support
565 Reorganize S/R call for overall time-stepping loop to facilitate
566 OpenAD revolve loop replacement
567 (new S/R main_do_loop.F)
568 o model/src:
569 - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
570 - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
571 ADAMS_BASHFORTH2.
572 o pkg/cheapaml:
573 - add new parameter (default=F, same as before) to disable full domain
574 (including land) periodicity in X & Y dir.
575 - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
576 prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
577 into single S/R CHEAPAML_TIMESTEP.
578
579 checkpoint64d (2013/02/17)
580 o pkg/monitor (angular momentum):
581 - do not add Eta contribution to the total AM if using rigid-lid;
582 - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
583 - horizontal discretisation: compute Zonal wind contribution separately for
584 each component (instead of from cell centered averaged) and use the 4
585 grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
586 - Check that AM is conserved with linear dynamics (momAdvection=F and linear
587 FreeSurf) if using vectorInvariant momentum.
588 o model/src (horizontal grid):
589 - move initialisation of all horizontal grid arrays to null value
590 from specific horizontal grid S/R to main S/R INI_GRID;
591 - add 2 new arrays to project model C-grid velocity on to zonal direction
592 (similar to AngleCosC & -AngleSinC but at U and V point location) and
593 compute them in S/R CALC_GRID_ANGLES.
594 o pkg/seaice: replace a hard coded parameter by a runtime parameter
595 SEAICE_JFNK_tolIter
596 o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
597 preconditioner for JFNK (run LSR into the overlaps as far as possible,
598 i.e OLx/y-2, but overwrite the solution in the overlaps)
599 - extend loop range in seaice_calc_viscosity
600 - add new parameters SEAICE_OLx/y (default = OLx/y-2)
601 - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
602 - slightly modify loops in tridiagonal solver lsr-preconditioner
603 - by default remove the extra exchange in seaice_preconditioner with a
604 replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
605 - modify offline_exf_seaice so that old results without RAS are reproduced
606 for output.dyn_jfnk.txt
607 in seaice_fgmres.F (unrelated to RAS)
608 - add a cpp-flag option for a re-ordered mapping (potentially more
609 efficient), but because this changes the results, turn it off by
610 default
611 - replace the save statement by local common blocks
612 o utils/matlab:
613 - fix tile-offset in rdmnc.m when output was produced using EXCH2.
614 - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
615 instead of local script "load_cs.m".
616 o pkg/seaice:
617 - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
618 to the scalarProductMetric and the unrolling. By chance this does not
619 change the verification experiment, because of the particular domain
620 decomposition
621 o pkg/diagnostics:
622 - change default missing_value from UNSET_RL to -999.
623 o pkg/layers: improve vectorization of layers_fluxcalc.F
624 - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
625 time spent in this routine by more than a factor of 3 on an NEC-SX8
626 - step 2: replace search algorithm by a bisection algorithm found in
627 Press et al. Numerical Recipes in Fortran. This algorithm can be
628 vectorized and finds the correct bin in approx. log2(Nlayers) steps.
629 For now, use this algorithm only for TARGET_NEC_SX defined.
630 - moved the search algorithm into a separate subroutine, that is kept
631 within the same file for automatic inlining.
632 - modified catching potential errors
633 o pkg/ecco:
634 - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
635 o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
636 - modifications for ALLOW_GENTIM2D_CONTROL
637 -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
638 -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
639 -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
640 -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
641 o model/src:
642 - account for moist thermodynamics in (dry) potential temperature equation;
643 update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
644 and cpl_aim+ocn.
645 - also switch to standard compiler (gfortran, was using ifort previously)
646 for fizhi-cs experiments reference output.
647 o pkg/ctrl:
648 - 1st step toward generic time-varying control variable (2D) via CPP option
649 ALLOW_GENTIM2D_CONTROL
650 - note new namelist ctrl_nml_genarr in data.ctrl
651 o verification/global_ocean.cs32x15:
652 - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
653 thsice calling sequence and update "output.icedyn.txt" output file.
654 o pkg/ptracers:
655 - from Ryan A.: code to allow to restart a tracer at regular time interval
656 specifying a reset frequency and a reset-phase (for each tracers).
657 o pkg/thsice:
658 - implement new sequence of calls for thsice+seaice:
659 previously: ice-Dyn,ice-Advect,ice-Thermo(thsice)
660 new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
661 - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
662 in CPP_OPTIONS.h) to recover old sequence;
663 - update diagnostics for Intermediate State thsice diagnostics: now filled
664 just before advection (instead of just after advection in old sequence);
665 - update output of experiment offline_exf_seaice (standard test);
666 - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
667 by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
668 o pkg/aim_v23:
669 - use tiled array for aim_CO2 and surface wind speed for export to coupler;
670 - use standard pkg/mdsio routines to read & write CO2 pickup file;
671 - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
672 - Implement new sequence of calls for seaice advection (with thsice and
673 seaice diffusion): do ice advection after ice-Thermodynamic (previously
674 was done before); change aim_do_physics.F (split the bi,bj loops block);
675 - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
676 o pkg/thsice:
677 - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
678 where just seaice diffusion is used without seaice-dynamics.
679
680 checkpoint64c (2013/01/18)
681 o pkg/seaice:
682 - add a parameter JFNKres_tFac that can replace JFNKres_t
683 (= JFNKres_tFac*JFNKresidual before JFNK solver)
684 - add a line search option to the JFNK solver
685 - move update of u/vIce and computation of initial residual into a separate
686 routine (same file); makes the code a little easier to read (?)
687 - the line search requires computation of the residual and for some reason
688 I cannot do the update of u/vIce at the beginning of the Newton loop
689 without changing the results, so we move computation of the new residual
690 also to the end of the Newton loop, even without the line search
691 o pkg/mdsio:
692 - write missing value (corresponding to undefined array value) to meta files;
693 skip this if missing value is one (UNSET_RL would be a better value for the
694 case of undefined missing value but it's current the default missing-value);
695 Also update mdsio_read_meta.F (reading timeInterval & missing-value).
696 o pkg/exf & thsice:
697 - for diagnostics purpose, fill-up and update Qsw array (+ fill the
698 diagnostics) even when SHORTWAVE_HEATING is #undef;
699 o verification/cfc_example:
700 - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
701 illustrate how to use it).
702 o verification/offline_exf_seaice:
703 in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
704 files to only one time-record.
705 in input.thermo: narrow the 2 bands of low initial ice-concentration near
706 N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
707 snapshot output; same mcPheePiston value as in thsice with
708 surf-current=0.2m/s.
709 in input.thsice: similar set-up as in input.thermo (channel with same seaice
710 initial conditions).
711 o verification/cfc_example:
712 - update file "data" with more standard choice (default rotationPeriod,
713 exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
714 set deltaTFreeSurf to deltaTtracer) and update the output.
715 o pkg/layers:
716 - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
717 - ensure that "layers_bolus" is switched to False when useGMRedi=False.
718 o verification/offline_exf_seaice:
719 - set all {field}period to zero for constant-in-time forcing (not tested
720 anywhere else).
721 o verification/offline_exf_seaice:
722 - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
723 - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
724 o model/src:
725 - implement Finite-Volume method for (hydrostatic) presure gradient
726 from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
727 o pkg/seaice: implement EVP* by Lemieux et al. (2012).
728 - In order to be compatible with the default EVP code, this requires changing
729 the EVP code around a little; and because any small change immediately
730 breaks the lab_sea.hb87 verification experiment, the reference output is
731 updated two times (each time the remaining aggrement was only 2 digits):
732 - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
733 - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
734 The adjoint test lab_sea.evp also needed to be updated.
735 - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
736 SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
737 a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
738 explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
739 INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
740 kept obscure, because I need to test it a little more.
741 o pkg/cheapaml:
742 - fix few incorrect type (_RL/_RS) in subroutine calls.
743 o pkg/seaice:
744 - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
745 to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
746 o model/src:
747 - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
748 change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
749 experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
750 o pkg/cheapaml:
751 - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
752 update output of experiment cheapAML_box.
753 - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
754 and set them only in one place (cheapaml_readparms.F).
755 - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
756 - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
757 and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
758 o model/src/the_main_loop.F:
759 - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
760 o pkg/seaice:
761 - remove legacy branch code.
762 - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
763 o verification/*/code*/SEAICE_OPTIONS.h:
764 - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
765 SEAICE_CAP_HEFF).
766 o pkg/cheapaml:
767 - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
768 to load new forcing fields.
769 - add missing "_d 0" where it's needed; + some editing (improve indentation).
770 - remove switch to "-r8" compiler option (no longer needed) in verification
771 cheapAML_box, keep same output (small trucation error differences).
772 o verification/offline_exf_seaice:
773 - add thermodynamics only test.
774 o verification/cheapAML_box:
775 - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
776 keep same output (same 14 digits for cg2d).
777 - switch on "-r8" compiler option (some numerical values are missing
778 the "_d 0") and update output (only 6 digits for cg2d were preserved).
779
780 checkpoint64b (2012/12/24)
781 o pkg/cheapaml:
782 - remove un-used variables (Qnet,EmPmR) from pickup files.
783 - store tendency of advected variables into cheapaml pickup file
784 and fix the AB-2 restart.
785 o verification/offline_exf_seaice and lab_sea adjoint:
786 - switch to new code (#undef SEAICE_GROWTH_LEGACY).
787 - switch to 4 time steps in offline, consistent with lab_sea.
788 - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
789 - update results after change of experiment seaice.
790 o pkg/seaice:
791 - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
792 parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
793 still defined since SEAICE_multDim needs to be set to MULTDIM value (from
794 SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
795 o model/src:
796 - add run-time parameter to select CG2D solver minimum-residual solution
797 (in case of a poor convergence).
798 o pkg/seaice/seaice_lsr.F
799 - move calculation of matrix coefficients into new
800 S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
801 file; the main purpose of this change is to be able to reuse the code
802 in S/R SEAICE_PRECONDITIONER
803 - modify the computation of the residual so that the mass of sea-ice
804 is not used twice; this simplifies the calculations, but since
805 the residual is never used except when LSR_mixIniGuess.ge.4---and this is
806 not tested in testreport---this does not affect the testreport results.
807 o verification/seaice_obcs:
808 - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
809 verification/lab_sea/input.salt_plume; changes results/output.txt*
810 o model/src:
811 - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
812 o pkg/seaice:
813 - improve description of parameters in seaice_fgmres.F and start
814 cleaning up the code
815 - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
816 second argument
817 - add a metric based on grid cell area to SEAICE_SCALPROD; update
818 results of offline_exf_seaice.dyn_jfnk
819 - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
820 o pkg/aim_v23:
821 - fix an other bug in dissipation heating (grid-cell area was missing).
822 o model/src + pkg/seaice:
823 - add global (multi-tile) linear solver for pair of tri-diagonal system
824 along X and Y lines, respectively for U and V component.
825 Note: 1) MPI and cube-exchange not yet coded.
826 2) probably not accurate for poorly conditioned / large size problem.
827 - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
828 default: not compiled and not used.
829 o pkg/seaice:
830 - first attempt at a multi-threaded fgmres solver for the JFNK solver:
831 introduce bi/bj loops and use global_sum_tile_rl instead of
832 mpi_allreduce in seaice_fgmres.F
833 - improve diagnostics output for fgmres solver (seaice_fgmres.F)
834 - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
835 - add a verification experiment for JFNK in offline_exf_seaice
836 o verification:
837 - change (for now, only fwd test) offline_exf_seaice experiment:
838 use a re-entrant channel with idealized coastline (trapezoidal shape)
839 at southern boundary to explore seaice dynamics and thermodynamics
840 with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
841 secondary test (input.thsice) use thermodynamics only with SST relaxation.
842 - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
843 o pkg/exf:
844 - disable "sstExtrapol" when Nr=1
845 o verification:
846 - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
847 to test pkg/cheapaml.
848 o pkg/aim_v23 & pkg/shap_filt:
849 - fix dissipation heating (erroneous gravity multiplication factor).
850 o pkg/seaice:
851 - remove unused field pressPre from jfnk solver
852 - rename two subroutines in seaice_preconditioner.F
853 o eesupp/src:
854 - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
855 o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
856 - remove wrong parts of the rhs and the lhs (were in there
857 because I did not understand the concept of this preconditioner)
858 - add an exchange between u- and v-sweep. This increases communication
859 by a factor of two but improves the convergence of jfnk. Ideally,
860 one would like the u- and v-sweep to be independent. So far within
861 undocumented ifdefs
862 - reorganize the extra computations for printing the residuals
863 o tools/genmake2:
864 - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
865 since it's not necessary (and was preventing to use MNC in some cases).
866
867 checkpoint64a (2012/11/16)
868 o pkg/autodiff:
869 - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
870 autodiff_readparms.F no longer depends on calling order (within
871 packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
872 rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
873 and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
874 o pkg/obcs:
875 - adding tidal velocity forcing capability to obcs
876 for usage example, see verification/seaice_obcs/input.tides
877 o pkg/seaice:
878 - turn the LSR-relaxation parameters WFAU/V into runtime parameters
879 SEAICE_LSRrelaxU/V
880 - introduce runtime parameter SEAICEetaZmethod (=0 by default)
881 o pkg/aim_v23:
882 - implement heating from friction (bottom friction and stratospheric drag).
883 o pkg/shap_filt:
884 - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
885 dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
886 o model/src:
887 - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
888 time-constant addMass field from file (addMassFile);
889 - support for heating due to friction (and Kinetic Energy dissipation):
890 add option, run-time switch and 3-D field array + support code ; each pkg
891 or S/R can add heating contribution (if there is a sink of KE); the sum is
892 accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
893 o pkg/seaice:
894 - complete merge of ITD code into seaice_growth.F
895 from MITgcm_contrib/torge/itd/code/
896 no verification so far, but Torge Martin tested
897 "1-D test case and Beaufort set up;
898 deliver okay results after 1 model year."
899 - complete merge of SEAICE_SIZE.h into all relevant routines
900 - move computation of eta at Z-points into calc_viscosities
901 + introduce global field etaZ
902 + add different methods for computing etaZ, for now the old
903 method (simple averages of eta to Z-points) is hardwired
904 + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
905 seaice_preconditioner
906 - simplify computations for SEAICE_ZETA_SMOOTHREG
907 - seaice_preconditioner:
908 + replace one remaining press by pressLoc (mistake)
909 + adjust printing of residuals
910 - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
911 + add (SEAICE.h) and rename some counters (initiliased in
912 seaice_init_fixed.F)
913 + add _BEGIN/END_MASTER (myThid) around print statements
914 + print total number of iterations and failures over SEAICE_monFreq
915 interval to STDOUT
916 - move control over output-messages by fgmres to seaice_jfnk to save
917 some operations
918 - move resetting initial guess for fgmres outside of seaice_fgmres_driver
919 in order to make restarts with sol .ne. zero (fgmres with restarts)
920 (seaice_jfnk.F, seaice_fgmres.F)
921 - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
922 a serious convergence problem when open boundaries are involved
923 o pkg/ggl90: fix computation of control volumes for the case of
924 ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
925 up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
926 o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
927 o pkg/autodiff
928 - Add inAdMode switch for SEAICEuseDYNAMICS:
929 SEAICEuseDYNAMICSinAdMode
930 (extend logic in ADAUTODIFF_INADMODE_SET)
931 o pkg/seaice
932 - Step 1 of merging ice-thickness distribution (ITD) code from
933 MITgcm_contrib/torge/itd/ (author: Torge Martin)
934 The code implements concept laid out in Thorndike et al. (1975);
935 code is enabled via CPP flag SEAICE_ITD
936 nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
937 code is not complete yet!!
938 - SEAICE_SIZE.h now included in almost all seaice routines
939 o verification (using seaice):
940 - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
941 global_ocean.cs32x15.seaice ; update results.
942 - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
943 - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
944 offline_exf_seaice (previously compiling B-grid).
945 o pkg/exf:
946 - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
947 to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
948 forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
949 o pkg/layers (adjust changes from Sept 19):
950 - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
951 this allows to remove "layers_maxNum" dimension from all layers arrays.
952 o pkg/layers (adjust changes from Sept 19):
953 - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
954 - snap-shot extended to all type of layers (not just the 1rst type);
955 - remove layers variables when corresponding CPP option is undef.
956 o pkg/layers:
957 - rename pkg/layers variable and add new output (layer exist & un-weighted
958 velocity in layer)
959 o pkg/seaice:
960 - simplify (?) ocean-drag coefficent computations by using
961 the same routine in all three solvers (saves some code lines)
962 - remove global fields DRAGA and DRAGS from C-grid code and
963 declare them locally in lsr.F (the only place where they are
964 still used)
965 - update AD output of lab_sea.evp (very sensitive anyway).
966 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
967 (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
968 and SEAICEuseJFNK=.true. A few things to note:
969 - involves a FGMRES, that is parallel but very inefficient,
970 because of many scalar products (global sums) in the Gram-Schmidt
971 orthogonalization method. Needs to be replaced. Original code
972 from J.-F. Lemieux
973 - preconditioner for FGMRES is a stripped down version of LSOR
974 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
975 preconditioner. For the preconditioner, the default is set to 10.
976 - Jacobian times vector is computed with finite differences
977 - marginally related to JFNK-solver: add a smooth regularization for
978 zeta with tanh that will improve convergence (Lemieux and Tremblay,
979 2009) for any implicit solver (not implemented for EVP because EVP
980 does not need this regularization in the first place). Define
981 SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
982 o eesupp/src:
983 - check in genmake2 that intrinsic S/R flush is available.
984 - add S/R to flush IO unit (if intrinsic S/R flush is available)
985 - flush standard & error msg unit before MPI termination
986 - if debugMode, flush IO unit after printing msg
987 o pkg/ctrl:
988 - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
989 to ctrl_set_unpack_xyz.
990
991 checkpoint64 (2012/10/09)
992 o pkg/shelfice
993 - in mom_fluxform.F, mom_vecinv.F:
994 CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
995 Bug fix KappaRU -> KappaRV
996 does not change verification/isomip but may change other setups
997 (presumably constant KappaRU=KappaRV)
998 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
999 o pkg/obcs:
1000 - fixed some indexing bugs in obcs_seaice_sponge.F
1001 - added obcs relaxation subroutines for HSALT and HSNOW
1002 - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
1003 o pkg/seaice:
1004 - add "multicategory" parameterization for snow in analogy to ice,
1005 default is off for now.
1006 o pkg/obcs:
1007 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
1008 see verification/seaice_obcs/input.seaiceSponge for example application.
1009 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
1010 index setting by master-thread. This fix multi-threads Pb in previous modifs.
1011 o pkg/layers :
1012 - add diagnostics to pkg/layers
1013 - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
1014 (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
1015 o pkg/generic_advdiff/gad_implicit_r.F :
1016 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
1017 o pkg/seaice/seaice_growth.F:
1018 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
1019 o pkg/obcs:
1020 - change default setting of OBCS_UVICE_OLD from defined to undef;
1021 - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
1022 in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
1023 - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
1024 - change OB null index value (OB_indexNone) to -99 ; this fix the problem
1025 with Southern & Western OB at a tile edge (at least in a simple set-up).
1026 o pkg/obcs:
1027 - change settings of OB index in case OB coincides with tile edge (shared by
1028 2 tiles), so that common OB location is registered by both tiles (instead of
1029 only 1). However, for Southern and Western OB, index value = 0 is not
1030 recognized as valid OB index (=default null value) and needs to be fixed.
1031 - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
1032 - new parameter "OB_indexNone" for null index value (for now, still zero)
1033 to replace hard-coded null index value of zero.
1034 o pkg/exch2:
1035 - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
1036 always check buffer-size (but outside the loop); move checking for valid
1037 index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
1038 print each tile and point connection only if |W2_printMsg|>= 2 and 3.
1039 o pkg/ctrl (pack & unpack):
1040 - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
1041 (locally defined) for different variables (+ remove the variable-specific
1042 file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
1043 (to be extended to other local file names in ctrl.h).
1044 o pkg/flt:
1045 - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
1046 o pkg/mdsio:
1047 - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
1048 o tools/genmake2:
1049 - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
1050 (added by Alistair in version 1.51 for building without make depend);
1051 - remove Header files list (H_SRC_FILES) from the dependence of targets
1052 ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
1053 place in version 1.23): this save going through staf when unrelated header
1054 file has been modified.
1055 Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
1056 "make depend" step, still need to do "make links" before "make adtaf".
1057 o eesupp/src (+ few pkg src files) & genmake2:
1058 - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
1059 - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
1060 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
1061 upper/lower case ; account for space between "#" and undef/define)
1062 o pkg/flt (with exch2):
1063 - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
1064 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
1065
1066 checkpoint63s (2012/09/05)
1067 o pkg/ecco:
1068 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
1069 - add more relevant #ifdef ALLOW_SMOOTH ones.
1070 - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
1071 o pkg/ctrl:
1072 - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
1073 ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
1074 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
1075 doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
1076 ctrlSmoothCorrel3D (new).
1077 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
1078 - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
1079 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
1080 controls when useAtmWind, and vice versa.
1081 - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
1082 - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
1083 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
1084 - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
1085 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
1086 - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
1087 replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
1088 o pkg/smooth:
1089 - remove un-necessary includes.
1090 - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
1091 Those CPP options were never defined, and not necessary.
1092 o model/src:
1093 - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
1094 - standard treatment of useSMOOTH.
1095 o pkg/autodiff:
1096 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
1097 useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
1098 o pkg/exch2:
1099 - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
1100 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
1101 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
1102 and tiles to process mapping.
1103 - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
1104 moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
1105 rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
1106 from w2_eeboot.F to w2_readparms.F.
1107 o eesupp/src:
1108 - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
1109 ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
1110 also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
1111 - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
1112 is defined (remove condition on usingMPI) to match cases where MPI_INIT
1113 has been called.
1114 - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
1115 - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
1116 (so that on 1 proc, get same myPid independently of usingMPI)
1117 - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
1118 useCubedSphereExchange with EXCH-1 (safer).
1119 - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
1120 o pkg/ggl90:
1121 - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
1122 used in ALLOW_GGL90_SMOOTH code.
1123 o pkg/flt:
1124 - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
1125 floats at the Southern end of the domain).
1126 o eesupp/inc:
1127 - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
1128 but not used (and not to be used) anywhere, just for documentation.
1129 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
1130 - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
1131 a) can damage previously written records in any other multi-record files.
1132 b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
1133 o tools/genmake2:
1134 - define variable MAKE within Makefile and use it in place of 'make';
1135 - update AD_CONFIG.h (if needed) before building any of the executable
1136 (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
1137 and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
1138 - always print usual warning comment 'this file is automatically generated'
1139 from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
1140 o pkg/cheapaml:
1141 - updated to correspond to the code used in accepted paper (Nico Wienders).
1142 o pkg/exf:
1143 added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
1144 ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
1145 and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
1146 o pkg/exf, autodiff, ctrl, ecco and seaice:
1147 remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
1148 o pkg/ctrl, ecco:
1149 allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
1150 Depending on useAtmWind, one is inactive, and the other is active (see
1151 exf_getffields.F/exf_getsurfacefluxes.F).
1152 o tools/genmake2:
1153 - improve error msg when failing in 2nd test of check_for_broken_Ff
1154 - fix option '-makefile' short-name (-mf according to genmake2 -help)
1155 - source local config file "genmake_local" just after processing the genmake2
1156 command arguments (previously done before processing arg).
1157 o pkg/grdchk:
1158 - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
1159 to this routine from cost_final has been dropped in g_cost_final)
1160 - improve printed information (more explicit msg, no longer using "print *,"
1161 fix fcpertminus printed value).
1162 o model/src:
1163 - move call to COST_INIT_VARIA out of packages_init_variables.F directly
1164 into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
1165 this prevents getting cost-funct reset in adinitialise_varia recomputations.
1166 o pkg/dic:
1167 - move initialisation of "freefe" array from from dic_biotic_forcing.F to
1168 fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
1169 o pkg/grdchk:
1170 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
1171 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
1172 o pkg/autodiff/ctrl/grdchk :
1173 - attempt to sort out what works and what does not,
1174 with regard to I/O, and to warn/stop accordingly.
1175 o pkg/grdchk:
1176 - attempt to fix grdchk in the case of useSingleCpuIO.
1177 - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
1178 statements were moved from grdchk_main.F and into
1179 grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
1180 - a global sum is applied to record numbers icvrec/layer
1181 out of grdchk_loc so that they be passed to I/O routines.
1182 o pkg/smooth:
1183 - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
1184 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
1185 o verification/testreport:
1186 - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
1187 - can also use compressed (gzip) reference output file;
1188 - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
1189 to be easier to collect by testreport.
1190 - update existing TLM output (half out-of-date by more than 3 yrs).
1191 - report NETCDF & LAPACK settings (from genmake2) in output dir.
1192 - report run-time in each individual summary (previously only for AD test);
1193 for TLM test, add also TAF version.
1194 - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
1195
1196 checkpoint63r (2012/08/15)
1197 o tools/genmake2:
1198 - fix Makefile for target ftlall (+ update files to clean after make ftlall)
1199 o pkg/ecco/ecco_cost_final.F :
1200 - fix fc print statements (to stdout and costfunction0000) so
1201 that the printed value is always after the global sum.
1202 o pkg/seaice/seaice_dynsolver.F :
1203 - fix ice strength assymptote at SEAICE_area_max<1
1204 (no change for the standard case of SEAICE_area_max=1)
1205 o some cleaning:
1206 - pkg source files: ensure that all *.F files from each pkg included the
1207 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
1208 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
1209 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
1210 includes;
1211 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
1212 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
1213 is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
1214 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
1215 - update option-file CPP_OPTIONS.h of all AD experiments:
1216 * no longer include PACKAGES_CONFIG.h ;
1217 * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
1218 * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
1219 including ECCO_CPPOPTIONS.h).
1220 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
1221 - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
1222 separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
1223 not necessary accurate).
1224 - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
1225 pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
1226 deliberately break compilation (a remainder that it needs to be customized)
1227 - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
1228 - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
1229 - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
1230 o tools/genamke2:
1231 - check for lapack.
1232 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
1233 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
1234 jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
1235 from both packages.
1236 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
1237 - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
1238 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
1239 of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
1240 o pkg/cost : add comments to explain special and/or untested setups.
1241 o pkg/exf:
1242 - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
1243 (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
1244 o verification/*/code_ad:
1245 mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
1246 - reccord when this file is included (define ECCO_CPPOPTIONS_H)
1247 - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
1248 allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
1249 o pkg/seaice :
1250 - added possibility to change ice strength/PRESS0 relationship to
1251 HEFF, according to the following run time parameters
1252 SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
1253 SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
1254 SEAICEpresH0 :: HEFF threshold for ice strength (m)
1255 o pkg/ggl90 :
1256 - added run time flag mxlSurfFlag to include the code that ensure
1257 mixing between first and second level (previously included as a comment)
1258 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
1259 - add test of newly added dumpAdByRec=T option where
1260 we write all records to one file per variable.
1261 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
1262 - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
1263 to check that this code is ok with taf and compiles in adjoint.
1264 o pkg/autodiff :
1265 - added run time param dumpAdByRec : ad dump format switch.
1266 If true then write all records to one file per variable.
1267 Else write one file per record (remains the default).
1268 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
1269 o pkg/seaice:
1270 - Added SEAICEuseTILT run time switch : if set to
1271 false then omit the tilt term in seaice dynamics.
1272 - Fix free drift calculation.
1273 o pkg/shelfice:
1274 When initializing SHELFICEDragQuadratic, set default to be
1275 consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
1276 but retain option to set it independently
1277 (inconsistenty spotted by Veronique Dansereau)
1278 o eesupp/inc:
1279 - in EEPARAMS.h, add real-type constant for some frequently used simple number
1280 (0,1,2,1/2), with name explicitly referring to RS/RL type.
1281 o model/src:
1282 - move balancing of relaxation terms to new S/R balance_relax.F.
1283 o pkg/autodiff:
1284 re-write active I/O high-level (control) S/R:
1285 - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
1286 - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
1287 - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
1288 MDS_READ/WRITE_FIELD); change loops to multi-threads.
1289 - update and merge active_file_control_slice.flow into active_file_control.flow
1290 - update the calls in lower level S/R (active_file.F, active_file_g.F and
1291 active_file_ad.F) keeping the argument list and function unchanged.
1292 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
1293 =.TRUE.") and remove high-level (control) _loc version (not called anymore).
1294 - new low-level active I/O routines, one for each type (RL/RS), for active var
1295 of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
1296 fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
1297 right type.
1298 o autodiff and RS=real*4:
1299 - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
1300 ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
1301 - change argument type of 3-D mask argument to _RS to match type in the call
1302 (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
1303 o pkg/thsice:
1304 - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
1305 - option to correct ocean fresh-water flux for imbalance of Atmos+Land
1306 fresh-water flux: uniform correction or proportional to local precip.
1307 o pkg/ctrl:
1308 - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
1309 - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
1310 ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
1311 - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
1312
1313 checkpoint63q (2012/07/30)
1314 o pkg/autodiff:
1315 note about monitor and snap-shot of ad-variables:
1316 a) need to apply ADEXCH before monitor or output of ad-vars to include
1317 overlap contributions (was done for adjDump but missing for monitor).
1318 b) since ADEXCH implies adding overlap values to interior array, machine
1319 truncation error is expected when adding an ADEXCH call in the middle of
1320 the time-stepping (although mathematically identical).
1321 modifs:
1322 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
1323 declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
1324 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
1325 apply ADEXCH before monitor or snap-shot of ad-variables:
1326 =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
1327 - implement new method (copy+adexch) for snap-shot and monitor of main model
1328 ad-vars (initially not used by default -> output unchanged).
1329 - change default (set to 2) to use new method and update few output_adm.txt
1330 with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
1331 and both tutorial_tracer_adjsens tests).
1332 - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
1333 and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
1334 o pkg/ctrl:
1335 enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
1336 generic control variables via
1337 #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
1338 Only required customization should be S/R ctrl_map_ini_genarr.F
1339 (routine in repository contains example)
1340 o pkg/exf:
1341 - fix and refine checking of surface-relaxation setting when using EXF
1342 o verification (adjoint exp):
1343 - reduce length of simulation by half for experiment global_ocean.cs32x15
1344 (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
1345 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
1346 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
1347 of KE that can occur with aggressive optimization
1348 + put quadratic bottom drag calculation in separated loops (only done if
1349 using bottomDragQuadratic)
1350 o model/src: CG2D_NSA
1351 - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
1352 and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
1353 - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
1354 change cg2d residual target to be expressed in Wunits (=> do not normalise
1355 RHS ; this fix global_max Pb with TAF); update output.
1356 o verification/tutorial_tracer_adjsens:
1357 improve parameter consistency (and get rid of warnings):
1358 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
1359 - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
1360 - use staggerTimeStep (for stability) in som81; use default rotation period.
1361 o pkg/exch2:
1362 - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
1363 reset to 0 = 1 long line in X)
1364 o pkg/mdsio:
1365 - fix reading of dimensions from meta file for large-size domain
1366 o model/src:
1367 - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
1368 - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
1369 Cubed-Sphere Exch with CS-corners inside the domain;
1370 make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
1371 globalArea and to set hasWetCSCorners.
1372 - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
1373 metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
1374 - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
1375 useCDscheme and useCubedSphereExchange).
1376 o pkg/seaice/seaice_growth.F :
1377 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
1378 for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
1379 when the previous code was not correct.
1380 - in all cases diagnoze the boundary condition mismatch to SIaaflux
1381 - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
1382 that term to QNET (essentially to set the melt/freeze water to 0degC).
1383 when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
1384 o verification/global_ocean.cs32x15/input.seaice :
1385 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
1386 - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
1387 - update results (output.seaice.txt) accordingly.
1388 o verification/lab_sea/input/data.seaice :
1389 - remove SEAICEheatConsFix, which is now be tested
1390 in global_ocean.cs32x15. The presently coded fix
1391 is only consistent with real fresh water + nlfs.
1392 - update results (output.txt) accordingly.
1393 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
1394 o AD_CONFIG.h file:
1395 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
1396 - remove #include "AD_CONFIG.h" from all included OPTIONS files and
1397 add it explicitly in each fortran src file where it is needed.
1398 motivation: header file AD_CONFIG.h is generated/modified after "make depend"
1399 thus introducing potentially wrong dependency; therefore, better to include
1400 it only where it's really needed, and after any other included OPTIONS file
1401 (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
1402 or ALLOW_TANGENTLINEAR_RUN).
1403
1404 checkpoint63p (2012/07/06)
1405 o pkg/autodiff:
1406 - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
1407 - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
1408 which are now read from new parameter file "data.autodiff" (inAdExact
1409 previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
1410 - add file "data.autodiff" in all verification/*/input_ad/ directories.
1411 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
1412 mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
1413 o verification/tutorial_tracer_adjsens/
1414 - add extra sub-verification which uses "SOM" advection scheme
1415 (2nd Order-Moment Advection Scheme, Prather Limiter) with
1416 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
1417 and in data:
1418 multiDimAdvection=.TRUE.,
1419 tempAdvScheme=81,
1420 saltAdvScheme=81,
1421 o model/src:
1422 - introduce ALLOW_BALANCE_RELAX which allow the removal
1423 of the global mean of relaxation terms by setting
1424 balanceThetaClimRelax and balanceSaltClimRelax
1425 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
1426 This case is now treated appropriately in seaice_growth.F
1427 o pkg/seaice:
1428 - do balanceEmPmR and balanceQnet based on the net fluxes
1429 (SItflux) that enter the ocean+ice system rather than QNET
1430 and EMPMR. Works best in real fresh water.
1431 - SIatmFW, SIatmQnet, and SItflux computations had to be moved
1432 out of the diagnotics bloc, and stored in global arrays.
1433
1434 checkpoint63o (2012/06/29)
1435 o vertical mixing schemes:
1436 - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
1437 - replace computation of density (in Function STATE1, opps_calc.F) by a call
1438 to S/R FIND_RHO_SCALAR
1439 - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
1440 and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
1441 affects output (vermix.ggl90) at truncation level.
1442 o testreport:
1443 - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
1444 (nSx,nSy) for the number of threads (from eedata.mth)
1445 o model/src:
1446 - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
1447 related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
1448 o verification/tutorial_tracer_adjsens/
1449 - compile with ALLOW_CG2D_NSA
1450 - run with nonlinFreeSurf=3
1451 - update reference output_adm.txt
1452 o tools/genmake2:
1453 - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
1454 refine usePROFILES switching off (only when NetCDF is not available).
1455 o verification (atmospheric set-up):
1456 - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
1457 o pkg/profiles : refine profiles and files handling.
1458 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
1459 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
1460 - changes to use model/src/the_main_loop.F rather than the ecco version
1461 in ecco type adjoint runs.
1462 o model/src:
1463 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
1464 - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
1465 - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
1466 o model/src:
1467 - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
1468 update output of test experiment bottom_ctrl_5x5.
1469 o pkg/generic_advdiff:
1470 - implement vertical bi-harmonic diffusion (for now, only for T & S and
1471 only explicitly).
1472 o verification/bottom_ctrl_5x5/
1473 update reference output (results changed quite some time ago,
1474 not sure when; but new reference results look ok in terms of grdchk)
1475 o verification/1D_ocean_ice_column/
1476 For verification purposes, the exact adjoint rather than an approx.
1477 should be used (e.g., to comare against F.D. or TLM).
1478 removed autodiff_inadmode*_ad.F routines in code_ad/
1479 Update results/ accordingly.
1480 o pkg/cal:
1481 - change cal_getdate.F so that output date is function of input time only
1482 (less ambiguous, not mixed up with input iteration number).
1483 - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
1484 o pkg/diagnostics:
1485 - implement calendarDumps also for stats-diags
1486 - implement calendarDumps also for snap-shot output (negative freq)
1487 - for now, ignores calendarDumps if non-zero phase-lag.
1488
1489 checkpoint63n (2012/06/04)
1490 o model/src:
1491 - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
1492 between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
1493 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
1494 similar to calc_r_star.F); update results of experiment internal_wave and
1495 tutorial_global_oce_in_p (affected @ truncation level).
1496 o pkg/shelfice:
1497 - add parameterisation of advective-diffusive flux into the ice shelf
1498 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
1499 - simply eps3/3a computation
1500 o eesupp:
1501 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
1502 between tiles, just fill-in edges assuming locally periodic subdomain) and
1503 add corresponding exchange subroutines (EXCH0);
1504 - new CG-solver version (_EX0) for disconnected-tiles special case.
1505 o model/src (CG-solvers):
1506 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
1507 (similar final residual output and max-Iter number as with standard version);
1508 - allows to store and use lowest-residual solution (standard & _SR versions);
1509 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
1510 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
1511 o eesup/src:
1512 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
1513 ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
1514 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
1515
1516 checkpoint63m (2012/04/27)
1517 o pkg/shelfice:
1518 - account for partical cells in surface level below ice-shelf for hydrostatic
1519 pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
1520 o ad test experiments:
1521 - update and rename to "ad_optfile.local" local AD-optfile specific to a
1522 particular adjoint verification experiment (in verification/*/code_ad/)
1523 o pkg/seaice & pkg/exf:
1524 - Part two of ECCO-CLIVAR code merges.
1525 Completes merge of seaice area relax. code.
1526 Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
1527 to be set in EXF_OPTIONS.h since this pkg controls its I/O
1528 (and avoids second CPP option in SEAICE_OPTIONS.h)
1529 - change default value of costIceStart & costIceEnd to a valid date.
1530 - add snowPrecip to HSNOW in seaice_growth
1531 o pkg/ptracers:
1532 - move ptracers summary and setup check into separated S/R ; add a check for
1533 valid PTRACERS_Iter0 value (error+stop or just warning).
1534 o pkg/cal (+ pkg/ecco):
1535 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
1536 as input; and for AD, unless both are not differentiable (e.g., k index)).
1537 o model/src:
1538 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
1539 is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
1540 temporary set to usingZCoords value (to be changed to F when using shelfice).
1541 - hydrostatic pressure: implement partial cell near the surface also for
1542 Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
1543 usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
1544 o pkg/ctrl/ctrl_init.F:
1545 - add a formal parameter to s/r ctrl_init_rec to print
1546 xx_$(ctrl_valiable)_file for easier debugging
1547 - move call of cal_* routines into the if-block where they are really
1548 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
1549 to specify a startdate
1550 o pkg/seaice:
1551 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
1552 global_ocean.cs32x15/code versions).
1553 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
1554 verification experiment global_ocean.cs32x15.seaice and update results.
1555 o pkg/exf:
1556 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
1557 (according to useExfYearlyFields).
1558 o pkg/cal:
1559 - move calendar setting & summary (previously in cal_readparams.F) into new
1560 S/R CAL_INIT_FIXED to be called later in the initialisation process, once
1561 length of the simulation is set (after SET_PARMS call); This is an attempt
1562 to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
1563 - For safety: keep a record of pkg/cal parameter settings status
1564 to allow to STOP if one pkg/cal S/R is called too early.
1565 - add a stop in all basic pkg/cal subroutines if called before setting is done.
1566 - modify cal_getdate.F: stop when nothing was returned;
1567 if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
1568 this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
1569
1570 checkpoint63l (2012/04/04)
1571 o pkg/bbl:
1572 - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
1573 update global_with_exf output.yearly.txt file.
1574 o pkg/cal:
1575 - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
1576 - remove 2 unsused and very short (1 line only) functions ;
1577 - remove unsused subroutines from AD-Diff list.
1578 o model/src:
1579 - start to implement clean wait to stop in initialization S/R (config_check.F,
1580 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
1581 o folowing PRINT_MESSAGE changes:
1582 - remove reminder multiple print to the same file (STDOUT) when multi-threads.
1583 o pkg/bbl:
1584 - modification so it can work with z*
1585 - replace deltaT with dTtracerLev(k) for asynchronous time stepping
1586 - global_with_exf/input.yearly verification; changes output.yearly.txt
1587 o eesupp/src:
1588 - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1589 writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1590 - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1591 # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1592 - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1593 - when using MPI, always set usingMPI=T ; set default accordingly and stop
1594 if not consistent.
1595 - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1596 argument is zero (in case called within single-thread section).
1597 o pkg/fizhi:
1598 clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1599 in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1600 o pkg/exch2:
1601 - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1602 activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1603 - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1604 but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1605 with bad ones coming from a not-yet-updated halo.
1606 This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1607 o pkg/frazil:
1608 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1609 http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1610 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1611 o verification/lab_sea
1612 * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1613 * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1614 * nTimeSteps 3 -> 4
1615 * changed reference output accordingly
1616 o pkg/ctrl:
1617 * fix ctrl_get_gen for xx_sst, xx_sss
1618 o pkg/fizhi:
1619 - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1620 update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1621 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1622 fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1623 clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1624 o pkg/gmredi:
1625 - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1626 o pkg/fizhi:
1627 - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1628 (old)aces open64 tuv test.
1629 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1630 o pkg/mom_vecinv:
1631 - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1632 set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1633 with non-lin free-surf).
1634 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1635 in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1636 some compilers (gfortran 4.6.0 on MacOS)
1637 o momentum:
1638 - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1639 & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1640 fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1641
1642 checkpoint63k (2012/03/17)
1643 o model/src:
1644 - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1645 flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1646 - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1647 (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1648 o model/src: solve_*diagonal.F
1649 - replace division with multiplication by inverse (similar to original version)
1650 update output of AD exp. global_ocean.90x40x15.
1651 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1652 to enable the use of the vectorized & differentiable solve_tridiagonal.F
1653 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1654 vertical advection (to get solve_tridiagonal tested in AD mode).
1655 o pkg/seaice: ECCO-CLIVAR merge:
1656 1. seaice AREA relaxation
1657 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1658 * runtime flag: SEAICE_tauAreaObsRelax
1659 2. modified global mean cost imbalance code: CPP option
1660 ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1661 o another iteration on solve_*diagonal.F
1662 Make choices independent of AUTODIFF
1663 Default will be the adjoinable vectorized version.
1664 Alternative choices are:
1665 * non-adjoinable original version with low memory footprint:
1666 #define SOLVE_DIAGONAL_LOWMEMORY
1667 * still adjoinable but does not vectorize (k as inner-most loop):
1668 #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1669 o testreport
1670 - add option to use a home made wrapper around "make"
1671 - remove MITGCM_IEEE env. variable (no longer active)
1672 o pkg/shelfice
1673 - improve computation of friction velocity for velocity dependent
1674 exchange coefficients: include velocities into SHELFICEBoundaryLayer
1675 block to average velocities vertically
1676 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1677 o Modify diagonal solvers, now three versions (upon request):
1678 #ifndef SOLVE_DIAGONAL_AUTODIFF
1679 1. default version (dating back a while ago)
1680 #else /* def SOLVE_DIAGONAL_AUTODIFF */
1681 # ifdef SOLVE_DIAGONAL_KINNER
1682 2. adjoinable version with k-innermost loop (G. Forget)
1683 # else
1684 3. adjoinable vectorized version of 2.
1685 # endif
1686 #endif /* SOLVE_DIAGONAL_AUTODIFF */
1687 All flags are currently set within routines, but could/should be moved to CPP-options.
1688 Array bounds for 1. are as before, for 2.,3. cover the entire domain
1689 (could be changed for 1. too).
1690 o verification/lab_sea (fwd):
1691 - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1692 use 7 categories (except hb87), new solve4temp params (except salt_plume),
1693 constant salinity (=4) or variable salinity (salt_plume) done through
1694 SItracer.
1695 o pkg/seaice:
1696 - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1697 - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1698 SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1699 from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1700 SEAICE_freeze got retired) but already better than previously with
1701 SEAICE_freeze=123456.7 deg.C;
1702 - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1703 (safer multi-threaded setting); always set SEAICEuseEVP;
1704 - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1705 SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1706 stop if multiple specifications for the same coeff; make sure default
1707 SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1708 o pkg/obcs:
1709 - allow to switch to upwind 1rst order advection scheme for the advective
1710 flux computation at the open-boundary; disabled for adjoint built.
1711 o pkg/ptracers:
1712 - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1713 - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1714 - add parameter to decide when to start a tracer; use internal flag to
1715 know which tracer to step-forward; switch this internal flag at the top
1716 of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1717 for adjoint built.
1718 o pkg/seaice:
1719 - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1720 - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1721 - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1722 o pkg/ecco:
1723 - fix writing of output file DiagnosCost_ClimSalt/Theta
1724 and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1725 o pkg/seaice:
1726 - add missing initialisation of COR_ICE array in dynsolver.F
1727 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1728 compiled either way, and is tested in all exps (multidim was only tested
1729 in lab_sea ad before).
1730 - cosmetic change to prepare for future addition of ITD. no change to results.
1731 no defaults change.
1732 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1733 - by lack of adequate verification experiments, I further used custom versions
1734 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1735 should be correct.
1736 - avoid recomputations in ad.
1737 o array initialisation in adjoint mode:
1738 1) pkg/mom_common/mom_calc_ke.F:
1739 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1740 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1741 part this initialisation is gone, resulting in Floating Point Exception
1742 (caught by open64 compiler with debug option).
1743 2) model/src/convective_weights.F
1744 set output convectCount over the full array range (instead of doing
1745 an update): this fix a similar issue when called within recomputation (adjoint)
1746 which could by-pass the initialisation (normally done in the caller S/R).
1747 o pkg/seaice:
1748 - final version of turbulent flux params, as agreed at MIT ice meet:
1749 SEAICE_mcPheePiston (default is ~ 0.000875)
1750 SEAICE_mcPheeTaper (default is 0.)
1751 SEAICE_frazilFrac (defualt is 1.)
1752 SEAICE_mcPheeStepFunc (default is false)
1753 - changes results at trunction error level
1754 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
1755 o added pkg/frazil:
1756 - see frazil_description.tex for details
1757 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
1758 o pkg/shelfice/shelfice_thermodynamics.F
1759 - fix exponents for velocity dependent exchange coefficients: change
1760 from 2/3(=0) to 0.66666666666666667
1761 - move computation of velocity dependent exchange coefficients into
1762 separate loop, so that it applies to both thermodynamics
1763 - move some divisions by constants out of loops
1764
1765 checkpoint63j (2012/02/16)
1766 o pkg/seaice:
1767 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
1768 - SItracer: added run time params, and allow coupling to ocn salinity.
1769 o pkg/seaice: remove (almost) all divisions by constants within loops
1770 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
1771 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
1772 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
1773 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
1774 o pkg/seaice :
1775 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
1776 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
1777 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
1778 - add permanent SItflux diag that corresponds to TFLUX but includes
1779 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
1780 - allow activation/testing of a fix for suspected missing term in
1781 ocn-ice heat budget (to be confirmed). To test this, you want to
1782 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
1783 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
1784 - no change in results, fwd or ad.
1785 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
1786 - switch to variable freezing point.
1787 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
1788 - bug fix : the sublimation term that was missing is now activated.
1789 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
1790 - bug fix : flooding sign term for SIsal0.NE.0.
1791 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
1792 o pkg/seaice:
1793 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
1794 is now the default, and the old default constant freezing point is recovered
1795 with SEAICE_tempFrz0 = -1.96,
1796 SEAICE_dTempFrz_dS = 0.,
1797 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
1798 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
1799 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
1800 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
1801 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
1802 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1803 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
1804 seaice_growth r149 for legacy branch (no results change).
1805 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1806 from I. Fenty).
1807 - results did not change except for global_ocean.cs32x15, mostly due to the
1808 switch to variable freezing point (see above item for detail).
1809 o pkg/thsice:
1810 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1811 seawater freezing in thsice_calc_thickn (not used).
1812 o pkg/seaice: turbulent flux term specification via run time params.
1813 - replace CPP switches with run time switches to facilitate testing
1814 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1815 GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1816 - added runtime parameter : SEAICEturbFluxFormula
1817 - move Mcphee constants to SEAICE_PARAMS.h
1818 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1819 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1820 remove seaice_summary call (moved to seaice_init_fixed)
1821 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1822 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1823 - seaice_summary.F : add missing report of read turbulent flux term set up
1824 and SITRACER.
1825 - seaice_check.F : check range; inform and stop if retired CPPs are used
1826 (incl. SEAICE_AGE).
1827 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1828 CPP switch, same computation as before for the different options.
1829 - change results at the truncation level.
1830 o pkg/seaice:
1831 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
1832 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
1833 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
1834 - update verification/*/input*/data.seaice:
1835 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
1836 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
1837 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
1838 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
1839 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
1840 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
1841 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
1842 difference in results only due to machine truncation.
1843 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
1844 MaykutPolySatVap; keep MIN_LWDOWN.
1845 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
1846 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
1847 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
1848 o pkg/salt_plume:
1849 - isolate saltPlumeFlux array exch into a specific S/R called from
1850 do_oceanic_phys.F
1851 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
1852 o verification:
1853 - move untested set-up to MITgcm_contrib/verification_other.
1854 o pkg/seaice:
1855 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
1856 o pkg/seaice:
1857 - seaice_solve4temp.F (keeping results unchanged):
1858 * add 2 future run-time params to select which saturation vapor pressure
1859 formula is used and how post-iteration fluxes are set.
1860 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
1861 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
1862 the linearized expression to stay consistent with tsurf finding.
1863 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
1864 can be < 0.
1865 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
1866 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
1867 conductive heat flux F_c , and add it explicitly when updating tsurf as
1868 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
1869 so that now F_ia has a consistent meaning through the entire routine.
1870 This causes differences at truncation level: update output of fwd exp.
1871 global_ocean.cs32x15.seaice.
1872 o pkg/seaice:
1873 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
1874 of arrays, sign/direction of fluxes; no effect on results.
1875 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
1876 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
1877 note: this should have been done before changing celsius2K default.
1878 - to keep results unchanged, add back old value of celsius2K in verification
1879 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
1880 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
1881 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
1882 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
1883 freezing temp is consistent with value in seaice_growth.F ; this causes
1884 differences at machine truncation level: update lab_sea AD output (3/4).
1885 o pkg/seaice:
1886 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
1887 and climsst/sss even when using seaice (to prevent calculation that might
1888 use SST on land); does not affect any verification exp.
1889 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
1890 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
1891 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
1892 over land (non-legacy code)
1893 o vectorize salt_plume package:
1894 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
1895 - this code computes plumebk everywhere (also over land), thus requires
1896 code to avoid divisions by zero and catch the case of kLev=Nr.
1897 - efficiency of salt_plume_frac is still sub-optimal
1898 o tools (genmake2):
1899 - fix makefile NAME specification (option: -makefile NAME) by adding
1900 "-f $MAKEFILE" in few places where it was missing including makedepend
1901 command (contribution from Paul).
1902
1903 checkpoint63i (2012/01/24)
1904 o model/src:
1905 - add factorized versions of some EOS code to find_rho.F,
1906 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
1907 o model/src:
1908 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
1909 - change default celsius2K from 273.16 to 273.15
1910 - to keep results unchanged, add back old value of celsius2K in verification
1911 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
1912 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
1913 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
1914 to make TAF generate vectorizable code
1915 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
1916 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
1917 have flags that do this more efficiently.
1918 o pkg/diagnostics/diagstats_calc.F
1919 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
1920 o pkg/obcs (with exch2):
1921 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
1922 and remove code (in obcs_readparms.F) which was based on EXCH of indices
1923 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
1924 o pkg/exf and seaice exp:
1925 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
1926 so that switching off area & heff advection flags does not affect results.
1927 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
1928 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
1929 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
1930 results of verification experiments: 1D_ocean_ice_column(fwd),
1931 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
1932 and offline_exf_seaice (all 4).
1933 o pkg/seaice:
1934 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
1935 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
1936 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
1937 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
1938 not multi-dim advection;
1939 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
1940 SHORTWAVE_HEATING #undef.
1941 o optim: make Makefile more robust (?)
1942 o pkg/obcs:
1943 * fix treatment of obcs_read_pickup for TAF
1944 o pkg/shelfice:
1945 * add missing initialisation of num_shifwflx
1946 * new adjoint verification exp. for isomip
1947 * change Prandtl and Schmidt numbers from generic formulations
1948 (in terms of model diffus. and visc.) to separate runtime
1949 parameters, with Holland and Jenkins (1999) default values.
1950 o pkg/exf (interpolation):
1951 - extended input field (2 rows) near the N & S poles:
1952 * fill in with the symetric value (when even Nb of data in longitude)
1953 * add average value at the poles only for scalar quantities ; for vector
1954 component interpolation, skip the averaging and keep duplicated values,
1955 unless the 2 components have same location (uvInterp=T) in which case
1956 interpolate the 2 components together using S/R EXF_INTERP_UV.
1957 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
1958 together: this allows to account properly for local orientation when
1959 averaging at N & S pole.
1960 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
1961 exf-interpolation near N & S poles. Undef by default.
1962 - add debug check/print on 1rst iter if debugLevel >=2.
1963 o pkg/exf:
1964 - change masking flags definition (no longer "parameter"), put them in
1965 common block and set them in S/R EXF_INIT_FIXED.
1966 - change recognized masking flag from s,u,v to c,w,s since the mask
1967 to use (maskC,W,S) depends on position on model grid and has little to
1968 do with scalar/vector difference; fix masking if using P-coordinates.
1969 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
1970 and update results of exp. global_with_exf (x2).
1971 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
1972 o pkg/obcs
1973 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
1974 o pkg/exf (interpolation):
1975 - assume periodicity in X only if input field cover full longitude range.
1976 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
1977 and should vectorise).
1978 - fix input lat of the 2 added row (in case we provide N.pole data).
1979
1980 checkpoint63h (2011/12/30)
1981 o pkg/seaice:
1982 - change declaration of UVM from _RL to _RS in order to get B-grid
1983 uIce,vIce monitor when _RS = real*4
1984 o pkg/offline:
1985 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
1986 - compute vertical velocity if not read from file (switch on exactConserv
1987 & staggerTimeStep);
1988 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
1989 o verification:
1990 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
1991 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1992 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1993 - update output of exp. global_ocean.cs32x15.viscA4 after changing
1994 grid-file angles (used here for coriolis-3d);
1995 - remove (or gzip) few files not needed to run fizhi-cs experiments.
1996 o pkg/exf (vector interpolation):
1997 - rotate vector component toward local grid-axis orientation using grid-angles
1998 (stored in GRID.h) instead of locally computed rotation angle; keep old code
1999 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
2000 o pkg/seaice:
2001 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
2002 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
2003 o pkg/PKG_OPTIONS.h files:
2004 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
2005 outside of the #ifdef ALLOW_THISPKG / #endif block.
2006 - update verification/*/code/PKG_OPTIONS.h files.
2007 o add a verification experiment (offline_exf_seaice/input.seaice) that test
2008 the B-grid LSOR solver
2009 o pkg/seaice: sort out emissivity and long wave radiation step 2:
2010 - add emissivity for snow and ice as new run-time parameters
2011 (unfortunately) that default to the corresponding exf values; this
2012 changes results in most verification experiments so that for backward
2013 compatibility these parameter have to be set explicitly to inconsistent
2014 values (ugly);
2015 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
2016 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
2017 until we agree how to handle this bug properly
2018 o pkg/exf (interpolation):
2019 - add a set of run-time param ({inputfield}_interpMethod), one for
2020 each interpolated input field, to select the interpolation method
2021 with a value of zero switching off the interpolation;
2022 - print interpolation parameters to standard output;
2023 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
2024 (to use instead runoff_interpMethod=0 in data.exf).
2025 - simplify default setting of interpolation parameters (for all fields,
2026 set position to match model grid cell-center position, leading to trivial
2027 interpolation in case of regular Lat-Lon grid) and fix for the case of
2028 non-uniform delY.
2029 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
2030 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
2031 this factor is absolutely required, because the lw exitance (= out-going
2032 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
2033 where the reflectivity rho = 1-emissivity for conservation reasons. Once
2034 this is established, we can remove the CPP-Flag (if we want to).
2035 o pkg/seaice:
2036 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
2037 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
2038 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
2039 what the name implies (and not emissivity*BoltzmannConstant), this means
2040 the old default value of 5.5e-8 now means
2041 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
2042 S/R exf_readparms
2043 - FV-discretization of the B-grid LSOR solver, turn on with
2044 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
2045 of the calling routine dynsolver, so that B and C-grid code look a
2046 little more alike.
2047 - fix index bugs in ostres.F (B-grid code)
2048 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
2049 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
2050 default for SEAICE_emissivity, if useEXF; requires setting a wrong
2051 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
2052 backward compatiblity
2053 o model/src: use sigmaR in calc_ivdc
2054
2055 checkpoint63g (2011/12/16)
2056 o pkg/seaice/seaice_growth.F:
2057 fix heat conservation of the coupled ocean-seaice system.
2058 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
2059 solid vs liquid water treatment is resolved via QNET.
2060 o pkg/seaice/seaice_growth.F:
2061 add missing term for sublimation in saltFlux, which was breaking conservation.
2062 o pkg/seaice/seaice_model.F:
2063 Remove this patholigical case treatment in evolution branch,
2064 where it is un-necessary and breaks conservation.
2065 Update global_ocean.cs32x15/results accordingly for
2066 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
2067 o model/src:
2068 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
2069 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
2070 o pkg/obcs:
2071 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
2072 tendency for temperature and salinity that is then applied to update
2073 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
2074 horizontal advection and diffusion contributions on the boundary (in
2075 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
2076 removing the mask in S/R timestep_tracer. The advantage of this approach is
2077 that the updated tracer values include contributions from the surface
2078 forcing and vertical diffusion.
2079 This modification changes exp4.stevens because of vertical diffusion.
2080 o model/src:
2081 change non-curvilinear grid setting to also work with exch2 + blank tiles:
2082 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
2083 face dimensions.
2084 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
2085 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
2086 and INI_SPHERICAL_POLAR_GRID.
2087 change test-experiment global_ocean.90x40x15:
2088 - split the domain in many more tiles (9x4 tiles of 10x10 each);
2089 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
2090 - update results of both test (std & dwnslp).
2091 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
2092 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
2093 o model/src:
2094 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
2095 and fix initialisation when using sigma-coords.
2096 o model/src:
2097 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
2098 to their current value at the beginning of forward_step.F": add a new run-time
2099 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
2100 - set doResetHFactors=T in the following test exp:
2101 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
2102 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
2103 and tutorial_global_oce_in_p (nonLinFS in p)
2104 o pkg/ecco
2105 - added IES cost term
2106 o verification/advect_xz
2107 - scale down the depth by 1/100 (from 200 km to just 2.km)
2108 - add secondary test using divergent flow, r-star and implicit vertical advection.
2109 - add note (check_conserve_TS.txt) and matlab script to check global
2110 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
2111 o pkg/rbcs:
2112 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
2113 o pkg/obcs (Stevens BCs):
2114 - fix various problems in the phase speed computations of the Stevens
2115 boundary conditions:
2116 - sign error for western and southern boundaries,
2117 - time tendencies were underestimated by factor of dTracerLev and some just
2118 zero (for multidim advection schemes) -> now estimate time tendencies
2119 from difference between previous (n) time level and the one before (n-1);
2120 this requires storing a field per tracer per boundary, also in the pickup
2121 files.
2122 - replace deltaTmom in cflMer/Zon computation with dTracerLev
2123 - set default phase velocity to cflMer/Zon
2124 - update verification experiment exp4.stevens
2125 o pkg/generic_advdiff (implicit_r):
2126 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
2127 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
2128 - fix implicit vertical diffusion or advection with NonLin FreeSurf
2129 (was using current recip_hFacC instead of future recip_hFacC): set future
2130 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
2131 solver S/R ;
2132 - fill diagnostics of vertical advective fluxes (computed from tendency)
2133 when using implicit vert. advection;
2134 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
2135 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
2136 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
2137 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
2138 o pkg/diagnostics:
2139 - add diags for T & S tendency which goes through Adams-Bashforth.
2140
2141 checkpoint63f (2011/11/30)
2142 o pkg/obcs/obcs_calc_stevens.F:
2143 - join some loops to reduce number of if-statements
2144 - fix a bug in code for northern and southern boundaries.
2145 o pkg/seaice/seaice_init_varia.F
2146 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
2147 caused zero ice-velocities for the B-grid code
2148 o pkg/seaice/seaice_init_fixed.F
2149 - fix a bug in the initialisation of the second metric terms
2150 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
2151 - this affects all seaice configurations with useCurviLinearGrid = .true.
2152 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
2153 = .true. (default)
2154 - the only verification experiment affected is global_ocean.cs32x15:
2155 icedyn, seaice, and seaice_dynmix (AD)
2156 o pkg/thsice/thsice_diagnostics_state.F
2157 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
2158 not contain garbage that can lead to surprises in diagstats_calc.F
2159 o model/src:
2160 - move bi,bj loops inside INTEGR_CONTINUITY ;
2161 - call INTEGR_CONTINUITY directly from forward_step.F
2162 (previously called from momentum_correction_step.F)
2163 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
2164 forward_step.F and pkg/ecco/the_main_loop.F
2165 o model/src/do_oceanic_phys.F:
2166 - reset addMass to zero only if useICEFRONT ;
2167 - separated k-loop for rhoInSitu calculation ;
2168 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
2169 and at constant T,S (= WdRHOdP);
2170 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
2171 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
2172 transport of locally-referenced potential density);
2173 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
2174 o gluemnc:
2175 - replace ncrcat with ncks when adding variables to *.glob.nc
2176 - change the way variables without record dimensions are handled so that
2177 files that have variables with and without record variables can be glued:
2178 add a record dimension with a new unique name to be able to differentiate
2179 between variable with and without a-prior record dimensions. Remove
2180 this record dimension before adding the variable to the *.glob.nc file.
2181 This procedure automatically works also for grid.*.nc files that do not
2182 have any record dimension.
2183 o verification/cpl_aim+ocn:
2184 - generate new reference output on baudelaire (gfortran, mpich2) (previously
2185 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
2186 o pkg/obcs/obcs_calc_stevens.F:
2187 - add code for northern and southern boundaries.
2188 - reorder some loops to save some operations and so that drFBar can be scalar
2189 o model/src:
2190 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
2191 truncation) and add diagnostics for Adams-Bashforth tendency increment.
2192 - update test-exp. AD output:
2193 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
2194 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
2195 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
2196 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
2197 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
2198 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
2199 tutorial_plume_on_slope.
2200 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
2201 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
2202 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
2203 does not even come with an F77 compiler anymore, this should not be
2204 a limitation
2205
2206 checkpoint63e (2011/11/06)
2207 o pkg/seaice adjoint of LSR:
2208 - substantially rework STORE dirs.
2209 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
2210 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
2211 and only perform SOLV_MAX_FIXED adjoint iters.
2212 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
2213 always goes to same record, meaning that the last forward field will be
2214 the one used in the adjoint - an approximation.
2215 - now produces non-zero LSR-related gradients, and acceptable gradients for
2216 An's zonal (x-z) test case (to be checked in)
2217 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
2218 (but these are screwed up by the thermodynamics in the first place);
2219 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
2220 output_adm.txt also reflects changes to seaice_lsr
2221 - global_ocean.cs32x15:
2222 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
2223 (output_adm.seaice.txt was updated)
2224 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
2225 (output_adm.seaice_dynmix.txt)
2226 o test-exp. exp4+stevens:
2227 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
2228 o pkg/seaice (lsr solver):
2229 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
2230 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
2231 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
2232 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
2233 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
2234 - compute (with new S/R) and print initial (+ free-driff sol. if available)
2235 and final residual of linearised system.
2236 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
2237 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
2238 o pkg/obcs: Stevens BCs (still only for east and west)
2239 - fix Stevens BCs by using intermediate velocities of previous
2240 time step as "baroclinic" contribution rather velocity of one grid cell
2241 inside the boundaries; more consistent but makes the entire treatment
2242 more complicated, requires new pickup files and two new S/Rs:
2243 obcs_copy_uv_n and obcs_save_uv_n
2244 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
2245 (undefined by default)
2246 - silently move computation of some grid factors into separate loops to
2247 save some recomputations
2248 - add a hack for non-linear free surface
2249 - add a verification experiment to exp4 that tests this code
2250 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
2251
2252 checkpoint63d (2011/10/25)
2253 o pkg/obcs + seaice-dynamics:
2254 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
2255 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
2256 values (consistent with an implicit method).
2257 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
2258 return to older implementation (same results as before); note that none of
2259 the "experimental" OBCS_SEAICE options are implemented in the new version.
2260 - switch test exp. seaice_obcs to use new version (update output).
2261 o pkg/seaice:
2262 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
2263 - add parenthesis in Water-Ice drag calculations (evp & lsr);
2264 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
2265 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
2266 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
2267 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
2268 o pkg/layers:
2269 - Include potential density as new coordinate (Thanks to David Munday)
2270 o pkg/dic:
2271 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
2272 carbonate computation/output to CALC_PCO2_APPROX
2273 o pkg/generic_advdiff
2274 - make TAF generate code that vectorizes:
2275 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
2276 o model/src:
2277 - improve vectorization also for adjoint code of
2278 solve_tridiagonal and solve_pentadiagonal. As this requires up to
2279 5 new 3D-fields, this code is only turned on for the combination of
2280 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
2281 for singular matrix check (only for TARGET_NEC_SX).
2282 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
2283 ALLOW_AUTODIFF. This flag now needs to be set outside of
2284 solve_tri/pentadiagonal.F
2285 o pkg/exf:
2286 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
2287 optional namelist EXF_NML_OBCS).
2288 - add many debug-print (to trace down where pkg/cal error msg comes from)
2289 o pkg/mom_vecinv/mom_vi_hdissip.F
2290 - rearrange loops so that vectorization is improved and in particular
2291 the adjoint routine vectorizes. The code is a little longer now, but I
2292 think easier to read.
2293 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
2294 o pkg/seaice:
2295 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
2296 o pkg/exch2:
2297 - alternative code (without tile x tile matrix) for cumulated (global) sum;
2298 used as default; keep using matrix version in adjustment.cs-32x32x1.
2299 o tools/build_options:
2300 - after merging some MPI and/or multi-threads specific optfiles so that
2301 the modified default optfile support both built (using genmake2 -mpi
2302 for the MPI built, using genmake2 -omp for OpenMP built),
2303 move now obsolete optfiles to tools/build_options/unsupported/
2304 (add copy of email sent to support list in doc/optfiles_changes.txt)
2305
2306 checkpoint63c (2011/09/28)
2307 o pkg/ebm:
2308 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
2309 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
2310 o pkg/seaice (SItracer pickup)
2311 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
2312 To be done:
2313 - thorough testing of missing fields in S/R seaice_read_pickup
2314 - thorough matching between generic tracers and specific fields used
2315 (e.g. volume-weighted age, area-weighted age, salinity, ...)
2316 o pkg/grdchk:
2317 - all procs calculate and print finite-difference gradient (for testreport)
2318 - change description output used by testreport;
2319 - AD testing: also compare and report Finite-difference gradient;
2320 => update all output_adm*.txt
2321 o test exp. global_ocean_ebm:
2322 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
2323 and turn on exactConserve; update (fwd) output.
2324 o pkg/seaice (LSR):
2325 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
2326 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
2327 * identical results with non-CS topology (but save up to half of EXCH calls)
2328 * no much changes in cs-32 verification tests since no ice at face edges
2329 (differences due to convergence criteria, since nb of iterations changed)
2330 * expect some differences on lat-lon-cap grid.
2331 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
2332 o pkg/exch2:
2333 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
2334 many tiles); until alternative coding is added, just add a stop.
2335 o pkg/kpp:
2336 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
2337 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
2338 o optfiles:
2339 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
2340 into corresponding standard one, which now support different build:
2341 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
2342 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
2343 o pkg/obcs (seaice):
2344 - add missing EXCH for uIce,vIce after applying OBCS;
2345 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
2346 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
2347 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
2348 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
2349 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
2350 and eedata.mth for MPI and mutlti-threaded testing.
2351 o pkg/flt:
2352 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
2353 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
2354 - fix pickup and trajectories + profiles output with multi-threads;
2355 - add parameter to select group of fields to write along trajectory and
2356 profile (default unchanged);
2357 - only call PORT_RAND* function when flt_noise <> 0;
2358 - add multi-threaded test for verification exp. flt_example.
2359 o eesupp/src:
2360 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
2361 - USE_OMP_THREADING: check that number of threads (from eedata) matches
2362 actual number (from env.var. setting).
2363 o pkg/ebm:
2364 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
2365 - add multi-threaded test for verification exp. global_ocean_ebm
2366
2367 checkpoint63b (2011/08/29)
2368 o pkg/ebm:
2369 - fix sign of runoff;
2370 - update directly forcing fields (Qnet,EmPmR) to use standard
2371 external_forcing_surf.F (remove ebm_forcing_surf.F);
2372 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
2373 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
2374 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
2375 - update global_ocean_ebm parameters file data and update output (fwd+ad).
2376 o verification/matrix_example:
2377 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
2378 MPI and mutlti-threaded testing.
2379 o pkg/matrix:
2380 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
2381 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
2382 - fix for multi-threaded (remove DATA statement);
2383 - use standard DIFFERENT_MULTIPLE function;
2384 - add MATRIX_OPTIONS.h
2385 o verification/matrix_example:
2386 To allow to split the domain in several tiles, change the domain size
2387 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
2388 Western side) of land points.
2389 o (*_)write_pickup:
2390 - fix few bugs in mypackage_read/write_pickup.F
2391 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
2392 array of length 1 (was caught by compiler syntax-check).
2393 o pkg/diagnostics (velocity potential solver):
2394 - fix initialisation of main diagonal matrix (for overlap values)
2395 o tools/build_options:
2396 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
2397 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
2398 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
2399 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
2400 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
2401 and use "-devel" testreport option for standard testing on baudelaire.
2402 o pkg/grdchk:
2403 - Assume that all gradient-check position are within the same tile
2404 corresponding to global indices (iGloTile,jGloTile) and that
2405 positions (i,j indices or nbeg) are local to this tile;
2406 - set tile local-indices and proc. number according to tile global-indices;
2407 - remove grdchkwhichproc from namelist (retired param);
2408 - send adjoint gradient to all procs so that all procs print it to STDOUT;
2409 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
2410 o adding package bbl (Bottom Boundary Layer)
2411 description in MITgcm/pkg/bbl/bbl_description.tex
2412 example/test experiment in MITgcm_contrib/bbl
2413 o adjoint verifications
2414 - changed 5 experiments to multi-tiles
2415 * global_ocean.90x40x15
2416 * obcs_ctrl
2417 * offline_exf_seaice
2418 * tutorial_dic_adjoffline
2419 * tutorial_tracer_adjsens
2420 changed reference output for those that crossed tile boundaries
2421 (changed choices of gradient check positions)
2422 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
2423 - temporary bug fix in grdchk_loc.F for obcs
2424 o genmake2 & testreport
2425 - add target "obj" (just for OBJFILES files) to Makefile;
2426 - add option to specify FEXTRAFLAGS on command line.
2427 o pkg/mypackage:
2428 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
2429
2430 checkpoint63a (2011/08/02)
2431 o pkg/diagnostics (velocity potential):
2432 - fix velocity-potential calculation when using OBCS: balance net inflow
2433 at each level (new S/R OBCS_DIAG_BALANCE).
2434 - fix some of the problems with OBCS in stream-function calculation.
2435 o pkg/exf/exf_readparms.F
2436 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
2437 EXF_NML_OBCS) more consistent, so that you need not have these lists
2438 in data.exf when they are not used.
2439 o optim/optim_readdata.F:
2440 - add some output about obcs variables that might help debugging
2441 - add a check about nvarlength
2442 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
2443 o pkg/diagnostics (velocity potential):
2444 - fix mask for OBCS (still problems in stream-function with OBCS);
2445 - add specific parameter (default = main code CG2D params) for solver;
2446 - in case of poor convergence, use solution corresponding to lowest residual.
2447 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
2448 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
2449 and should be avoided where possible.
2450 o model/src (rStar):
2451 - include r* effect on reference-state (PhiRef) in totPhiHyd
2452 (so that it's really the potential anomaly at the cell center);
2453 affect solution only if z* with full pressure in EOS.
2454 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
2455 update output (because of z* in totPhiHyd and viscA4 changes);
2456 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
2457 @ constant r) until interpolation at constant r is implemented.
2458 o pkg/diagnostics
2459 - fix RCENTER diagnostics in case cell center is not at interface middle
2460 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
2461 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
2462 that THETA and SALT are "conservative temperature" and "absolute
2463 salinity"
2464 o pkg/ctrl
2465 - fix computation of endrec in s/r ctrl_init_rec
2466 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
2467 o pkg/seaice/seaice_growth.F
2468 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
2469 remove then obsolete STORE directives
2470 - fix STORE directives for tice and tices, so that only the
2471 appropriate part of the fields are stored (and not the entire
2472 field); update global_ocean.cs32x15.seaice AD output.
2473 - cosmetic changes: adjust CPP flags and indentation for better
2474 legibilty
2475 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
2476 Chris Wilson)
2477 o pkg/gmredi:
2478 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
2479 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
2480
2481 checkpoint63 (2011/07/11)
2482 o pkg/exch2:
2483 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
2484 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
2485 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
2486 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
2487 o pkg/diagnostics:
2488 - deal with pairs of post-processed diags which are computed together; in
2489 particular, re-order list of diags within 1 file to save 2nd computation.
2490 - add S/R to compute velocity stream-function (called after velocity-potential
2491 calculation) from divergence free transport -> new diagnostics "PsiVEL".
2492 - add parameter to select grid-point location where PsiVEL == 0.
2493 o eesupp/src:
2494 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
2495 (specific S/R needed with exch2 topology - for now, just print an error msg)
2496 o pkg/shelfice
2497 - Implement friction velocity-dependent transfer coefficients following
2498 Holland and Jenkins, JPO, 1999
2499 Original code by M. Losch with small modifs.
2500 Enable with CPP option SHI_ALLOW_GAMMAFRICT
2501 and runtime flag SHELFICEuseGammaFrict
2502 o verification lab_sea & global_ocean.cs32x15:
2503 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
2504 does not miss some dependencies (but is slower) and also works with many files
2505 (default makedepend limitation for AD built).
2506 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
2507 o pkg/diagnostics:
2508 - add run-time parameter "useMissingValue" (def=False) to fill land-point
2509 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
2510 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
2511 - Extend the use of "missing_value" setting from data.diagnostics for the case
2512 of counter-diagnostics (where fraction-weight is zero). This applies both to
2513 MNC and MDS output files.
2514 o pkg/seaice/seaice_growth.F:
2515 - add 'a priori' cap of latent heat flux based on actual mass considerations
2516 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
2517 non-legacy seaice_solve4temp.
2518 - add diagnostic of the residual sublimation freshwater flux (the freshwater
2519 flux taken from the ocean if the total actual latent heat fluxes exceed
2520 the maximum)
2521 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
2522 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
2523 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
2524 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
2525 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
2526 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
2527 o verification 1D_ocean_ice_column:
2528 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
2529 update results
2530 o pkg/diagnostics:
2531 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
2532 which are not filled-up but computed from other diags ; In this case, the mate
2533 diag points to the primary (filled-up) diag to used for post processing.
2534 - Update Velocity-potential computation using post-processed diag framework.
2535 ==> Change the ordering of fields and time-periods in MDS output file
2536 when using periodic averaging: now writes one time record with the full set
2537 of fields for this time period, then the next time reccord (it used to be
2538 one field with the full set of time records then the next field).
2539 Note: this is now similar to NetCDF (MNC) output file. <==
2540
2541 checkpoint62z (2011/06/21)
2542 o adjoint monitor:
2543 - Add adjoint monitor output for packages exf, seaice
2544 and update relevant testreport output
2545 o pkg/seaice:
2546 - re-order diags inits so that they appear in order in available_diagnostics.log
2547 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
2548 area/heff/hsnow preceeding thermodynamic growth/melt.
2549 - modified diag: SIdA; output actual effect, as the description states.
2550 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
2551 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
2552 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
2553 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
2554 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
2555 - added diagnostics for seaice generic tracers (SItr*).
2556 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
2557 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
2558 I. Fenty: 18-Jun-2011:
2559 Minor changes to seaice package:
2560 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
2561 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
2562 - Differentiated "regularization variables" from "floor variables"
2563 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
2564 * hiceMin became SEAICE_hice_reg (old hiceMin)
2565 (with _reg meaning regularization variable)
2566 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
2567 so as to ensure energy conservation when going between phases
2568 - A22 was not used anywhere
2569 2) Changed regularization procedure for heffActual and hsnowActual to ensure
2570 well-boundedness and smooth adjoint in seaice_growth.F
2571 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
2572 because the old regularization always set heffActual >= 0.05 cm
2573 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
2574 on AREA when HEFF > 0.
2575 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
2576 requiring that DISABLE_AREA_FLOOR *not* be defined
2577 Affected verifications:
2578 - 1D_ocean_ice_column (output.txt output_adm.txt)
2579 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
2580 o pkg/diagnostics:
2581 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
2582 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
2583 (was _RL, now integer) with option = 0 to retrieve all levels.
2584 - add pieces of code to compute velocity potential at each level (new diagnostics
2585 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
2586 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
2587 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
2588 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
2589 and in diagnostics_fract_fill.F (do not need a valid pointer for the
2590 diagnostics counter-mate); check that definition of counter-diagnostic
2591 includes a valid counter-mate (in diagnostics_set_levels.F).
2592 o model/src (rStar):
2593 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
2594 affect solution only if z* with full pressure in EOS;
2595 update output of test-exp global_ocean.90x40x15.
2596 o pkg/seaice:
2597 - introduce siEps=1e-5 parameter
2598 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
2599 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
2600 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
2601 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
2602 as well as ice cover age and ridging index (attached to AREA).
2603 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
2604 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
2605 Up to SItrMaxNum=3 tracers can be used simultaneously.
2606 o pkg/salt_plume:
2607 -introduce SPsalFRAC run time parameter that sets the fraction of the
2608 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
2609 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
2610 o model debug options:
2611 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
2612 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
2613 - Refine debug-msg printing selection (3 new levels):
2614 debugMode : controls printing of debug messages (sequence of S/R calls).
2615 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
2616 debLevZero = 0 ; /* level of disabled aux. msg printing */
2617 debLevA = 1 ; /* level of minimum aux. msg printing */
2618 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
2619 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
2620 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
2621 debLevE = 5 ; /* level of extensive debug printing */
2622 New debugLevel default: with default debugMode value (=F),
2623 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
2624 and if debugMode=T, default debugLevel = 4 (debLevD).
2625 Relation with previous settings:
2626 debLevB (=2) corresponds to former debLevA (=1)
2627 debLevD (=4) corresponds to former debLevB (=2)
2628 Note:
2629 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
2630 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
2631 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
2632 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
2633 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
2634 o pkg/obcs:
2635 - change OBCSfixTopo default from True to False (should not change the results);
2636 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
2637 o pkg/thsice:
2638 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
2639 2nd layer seaice sublimation (unlikely to happen)
2640 - use Interior mask for OBCS in thsice_advection.F (similar to what is
2641 done in gad_advection & seaice_advection).
2642 o adjoint:
2643 bug fix spotted by Gael Forget:
2644 seaice_advection and thsice_advection still had
2645 legacy CPP options to avoid CS corner updates for adjoint
2646 o pkg/seaice:
2647 => Change some of the defaults (2011/05/29):
2648 - change SEAICEuseFluxForm default (from False to True)
2649 - change DIFF1 default (from 0.004 m/s to 0. m/s)
2650 And print warnings if DIFF1 is not set in data.seaice and centered
2651 avection scheme is used without any diffusion.
2652 also:
2653 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
2654 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
2655 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
2656 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
2657 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
2658 update results of test exp.:
2659 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
2660 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
2661 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
2662 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
2663 seaice_obcs: output (SEAICEuseFluxForm=T)
2664 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
2665 for standard fwd & AD lab_sea tests (to keep the same output).
2666 o pkg/seaice/seaice_growth.F:
2667 - use Ian Fenty's capping formulas for actual ice
2668 thickness thoughout EVOLUTION branch.
2669 - put treatment pathological case #2) in CPP brackets
2670 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
2671 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
2672 o pkg/seaice:
2673 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
2674 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
2675 also pass fac as a param, which can be 1. (to update the tendency
2676 field) or the time step (to update the field itself).
2677 - seaice_advdiff.F: for multidim, call seaice_diffusion with
2678 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
2679 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
2680 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
2681 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
2682 o pkg/seaice:
2683 diffusion with centered advection scheme (diffus.F & advect.F):
2684 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
2685 to just compute the laplacian of input-field.
2686 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
2687 - fix flux-form version in diffus.F to conserve tracer.
2688 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
2689 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
2690
2691 checkpoint62y (2011/05/26)
2692 o pkg/seaice:
2693 - seaice_growth.F : in EVOLUTION branch, always include
2694 a_QSWbyATM_cover in qnet (as it should be).
2695 - verification/global_ocean.cs32x15 : update results accordingly
2696 (output.seaice.txt output_adm.seaice.txt).
2697 o pkg/seaice + obcs:
2698 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
2699 equivalent of assuming no tracer gradient outside the OB region.
2700 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
2701 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
2702 after changes above);
2703 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
2704 only at OB location (instead of over a band of OLx width).
2705 o pkg/seaice:
2706 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
2707 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
2708 o pkg/obcs:
2709 - split header file "OBCS.h" into 4 separated files:
2710 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
2711 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
2712 (contain no conditional statement which depends on OBCS options).
2713 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
2714 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
2715 o ctrl, cost, grdchk & autodiff pkgs:
2716 - make options file more standard (like other {PKG}_OPTIONS.h file but
2717 with AD_CONFIG.h); clean-up some of the included header files.
2718 o pkg/obcs:
2719 - do not mask tracer when applying OB (tracer == 0 could generate problems)
2720 - apply tracer OB values to tracer field only at OB location (instead of
2721 over a band of OLx width)
2722 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
2723 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
2724 obcs_apply_tloc.F & obcs_apply_sloc.F
2725 o obcs in model/src:
2726 - call OBCS_APPLY_W only if NonHydrostatic.
2727 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
2728 - reset dEtaHdt and wVel to zero outside OB interior region ;
2729 - leave tracer unchanged outside OB interior region: This has no effect
2730 on the solution but just to prevent unrealistic tracer value outside OB.
2731 - zero out velocity outside OB interior region: This has no effect on
2732 the solution but just to prevent unrealistic velocity outside OB.
2733 o obcs and non-lin free-surf:
2734 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
2735 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
2736 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
2737 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
2738 update results of test-exp. exp4(nlfs).
2739 o exp4 (nlfs) test-exp:
2740 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
2741 with NonLin-FreeSurf); update output.nlfs.txt
2742 o obcs and 2d/3d solver norm:
2743 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
2744 and outside OB interior region (will allow to place OB further inside the
2745 domain). Depending on the domain, can affects cg2d-Norm (previous
2746 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
2747 and cg3d-Norm (previous Norm was computed before canceling OB terms),
2748 e.g. in tutorial_plume_on_slope.
2749 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
2750 o pkg rbcs:
2751 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
2752 - add capability to apply relaxation to horizontal velocity uVel & vVel.
2753 o pkg/grdchk: add gradient check for control variable xx_shifwflx
2754 o pkg/shelfice/shelfice_init_fixed.F
2755 fix CPP-flag combinations
2756 o pkg/seaice: Merge iceage code of Pierre Rampal
2757 * update/change/correct ice age calculations
2758 * add age updates for pathological cases
2759 Probably needs more testing...
2760
2761 checkpoint62x (2011/05/13)
2762 o pkg/mom_vecinv:
2763 high-order vorticity scheme: use interior masks (maskInW & S)
2764 to zero-out (outside OB) gradient of vorticity.
2765 o verification exp.:
2766 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
2767 hs94.128x64x5 and seaice_obcs ; update results.
2768 o pkg/obcs:
2769 fix bug in OBeta for YZ sections in obcs_exf_load.F
2770 o pkg/ctrl, pkg/shelfice, and optim:
2771 - add new control variable xx_shifwflx (fresh water flux underneath ice
2772 shelves). This is almost as tedious as obcs-ctrl, because the
2773 variables needs its own mask.
2774 - add a cost function term that penalizes the deviation of xx_shifwflx
2775 from the first guess (zero) in analogy to other control variables
2776 o pkg/shelfice:
2777 - start basic adjoint
2778 o pkg/ctrl:
2779 - remove extra 2D field "for good measure" when initializing in
2780 ctrl_set_globfld_[xy/xz/yz].F
2781 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
2782 - improve error messages in ctrl_set_unpack_*
2783 o OBC implementation in momentum:
2784 use interior masks (maskInC,W & S) in momentum S/R:
2785 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
2786 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
2787 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
2788 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
2789 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
2790 (and also with Leith/Smagorinsky harmonic-viscosity).
2791 Update output of experiment dome and exp4 (+nlfs).
2792 o exp4 test-exp:
2793 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
2794 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
2795 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
2796 time-varying OB at Western-side for wVel (NonHyd); update output.
2797 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
2798 and biharmonic-viscosity ; also use prescribed time varying OB.
2799 o pkg/obcs:
2800 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
2801 o model/src:
2802 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
2803 - initialise startTime & nIter0 with unlikely values: allows to set one
2804 from the other without ambiguity.
2805 o seaice_obcs test-exp.:
2806 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
2807 o pkg/obcs:
2808 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
2809 no longer needed with maskInC,W,S in pkg/generic_advdiff.
2810 o pkg/seaice:
2811 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
2812 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
2813 - fixed bug in the initialization of sea ice salinity variable HSALT
2814 in seaice_init_varia.F (removed dependence on ICE2WATR)
2815 o fizhi-cs test exp.:
2816 switch reference output convention for these 2 non-standard test-exp,
2817 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
2818 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
2819 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
2820 o model/inc:
2821 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
2822 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
2823 o pkg/seaice:
2824 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
2825 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
2826 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
2827 and initial HSALT
2828
2829 checkpoint62w (2011/04/26)
2830 o pkg/mom_fluxform:
2831 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
2832 - use parameter "sideDragFactor" in no-slip BC side-drag part.
2833 - update output of exp. global_ocean.90x40x15
2834 o pkg/mom_vecinv:
2835 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
2836 o update seaice exp.:
2837 use more consistent parameter values (remove "backward compatability only":
2838 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
2839 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
2840 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
2841 o update test-exp global_ocean.90x40x15:
2842 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
2843 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
2844 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
2845 o turn on zStar & viscA4 in standard set-up (dir input/)
2846 and update output files: output.txt & output.dwnslp.txt
2847 o new AD-test experiment: obcs_ctrl
2848 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
2849 o pkg/dic:
2850 fix two bugs in handling water vapour pressure in carbonate chemistry
2851 and air-sea fluxes. Found by Val Bennington and Galen McKinley
2852 (add DIC Option = WATERVAP_BUG to recover old results)
2853 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
2854 o adding allowInteriorFreezing option to check for water below freezing point
2855 at depth and bring the negative heat anomaly to the surface level
2856 o pkgs _fields_load:
2857 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
2858 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
2859 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
2860 rbcs to get interpolation weights and time reccord number.
2861 - fix multi-threading in aim_fields_load.F
2862 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
2863 o external_fields_load:
2864 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
2865 interpolation weights) to use in a periodic time-series ; do not divide by
2866 time-step to convert to integer:
2867 - this fixes case where externForcingPeriod is not multiple of time-step
2868 (Thanks to Christopher L. Wolfe)
2869 - this fixes case where externForcingPeriod is an odd multiple of time-step
2870 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
2871 store index of time-record which is currently loaded:
2872 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
2873 - needed for the adjoint but not yet used because of extensive recomputations;
2874 (to be fixed soon)
2875
2876 checkpoint62v (2011/04/02)
2877 o verification/1D_ocean_ice_column added to test Ian Fenty's
2878 pkg/seaice_growth.F modifications for improving sea ice code differentiability
2879 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
2880 (new velocity statistics after changing maskInW & maskInS definition)
2881 o pkg/generic_advdiff with OBCS:
2882 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
2883 equivalent to assumption of no tracer gradient outside the OB region.
2884 This will affect the results if using obcs+biharmonic diffusion.
2885 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
2886 o pkg/obcs:
2887 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
2888 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
2889 in Interior region. No impact on solution but affects Velocity monitor stats.
2890 o pkg/ptracers (adjoint)
2891 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
2892 tape file for each tracer
2893 o model/inc/src and pkg/autodiff: add parameters that allow to turn
2894 of parts of the adjoint code at run time. For now, there are only
2895 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
2896 parameters are set in data.pkg.
2897 This is the lazy coward's version of doing this, but still useful for
2898 debugging. In order to do it right, everything needs to be moved to
2899 pkg/autodiff.
2900 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
2901 the end; this fixes the adjoint balancing code for open boundaries.
2902 o pkg/ctrl:
2903 - change behavior of xx_${varname}period to be analogous to exf-conventions:
2904 xx_${varname}period = 0., means time-independent control part
2905 xx_${varname}period = -12., means one-year-periodic monthly control part
2906 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
2907 clean up ctrl_init a little, remove unused variables
2908 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
2909 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
2910
2911 checkpoint62u (2011/03/15)
2912 o model/src:
2913 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
2914 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
2915 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
2916 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
2917 o pkg/ctrl/obcs/ecco:
2918 - remove obsolete, unused, and partially broken code:
2919 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
2920 ALLOW_CTRL_OBCS_BALANCE
2921 - put a stop statement into ecco/cost_obcsvol.F, but also add
2922 cost_obcsvol to ecco_ad_diff.list
2923 o pkg/ecco: fix counting cost function contributions for obcs (code
2924 by Matt M.) and diffkr for diagnostics
2925 o pkg/ecco, pkg/ctrl, pkg/grdchk:
2926 add cost penalty terms for initial uvel, vvel, eta controls
2927 and I/O for prior error files
2928 o pkg/mdsio:
2929 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
2930 (new argument) to check for tiled file in mdsioLocalDir : this fix the
2931 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
2932 o pkg/ctrl:
2933 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
2934 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
2935 unused and superfluous variables
2936 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
2937 o pkg/ecco
2938 - enable adjoint of Stevens OB
2939 o pkg/ctrl/ecco/grdchk:
2940 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
2941 Fortunately, we do not have any tests for the numerous cpp-flagged
2942 option of "obcs as control parameters" so we will never know
2943 if this is an improvement (but at least now things compile).
2944 - remove an obsolete initialization from ecco_cost_init_barfiles.F
2945 - fix some problems within never used ifdefs to make the code compile
2946 o pkg/obcs:
2947 - Refine Interior mask definition to work with more complex OB (e.g.
2948 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
2949 read in Interior mask from file. Check if Interior mask is consistent
2950 with OB list of indices.
2951 o pkg/seaice
2952 - beginning code for a seaice tracer package,
2953 but currently only used for seaice age: SEAICE_AGE
2954 SEAICE_num = 4
2955 iTracer = 1: area-weighted ice age
2956 = 2: volume-weighted ice age
2957 = 3, 4: template for one-year vs. multi-year ice
2958 data.seaice has new namelist SEAICE_PARM03 for arrays related to
2959 SEAICE_num
2960
2961 checkpoint62t (2011/03/05)
2962 o pkg/obcs:
2963 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
2964 then normal component. This ensures that the normal component is set
2965 correctly even when it conficts with tangential setting from an other OB.
2966 Affects results of test-experiment seaice_obcs: update the output.txt
2967 o pkg/obcs:
2968 - add code to monitor statistics of dynamical fields at OB.
2969 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
2970 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
2971 - change default: balance the Net inflow through all OB (instead of balancing
2972 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
2973 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
2974 to match Nortern OB inflow (OBCS_balanceFacN=0).
2975 o pkg/seaice:
2976 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2977 o pkg/seaice (seaice_growth v 1.113):
2978 - reverting seaice_growth to v 1.111 in order to have code with exact bit
2979 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
2980 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
2981 runtime flag SEAICEareaFormula is kept but is inactive
2982 o model/src:
2983 - add new param to scale curvilinear grid distance and area when using
2984 a different sphere radius from the grid-files.
2985 - test/check multi-threads EXCH applied to local variable (cg2d_x)
2986 o adjoint:
2987 - enable adjoint of Stevens OB
2988 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
2989 (a bit delicate because of potentially modified adj. common block structure;
2990 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
2991
2992 checkpoint62s (2011/02/15)
2993 o pkg/seaice (seaice_growth v 1.112):
2994 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
2995 computing the ice cover tendency from effective thickness tendencies. Include
2996 Ian Fenty's formula.
2997 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
2998 SEAICEareaFormula.
2999 - simplify notations for the various d_HEFF/d_AREA terms.
3000 o pkg/gmredi:
3001 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
3002 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
3003 add a verification test-run (front_relax.bvp) to test GM_useBVP.
3004 o pkg/seaice (seaice_growth v 1.111):
3005 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
3006 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
3007 also melt ice.
3008 o pkg/seaice:
3009 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
3010 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
3011 o pkg/cheapaml:
3012 - from Nico Wienders: New version of this package.
3013 o pkg/flt:
3014 - add CPP options to prevent floats to re-enter the opposite side of
3015 a periodic domain (default: keep periodicity)
3016 o pkg/gmredi:
3017 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
3018 (needed for multi-dim advection).
3019 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
3020 o model/src:
3021 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
3022 o tutorial_tracer_adjsens
3023 - extend to NLFS and replace maskC by hFacC
3024 (change reference output accordingly)
3025
3026 checkpoint62r (2011/01/24)
3027 o testreport:
3028 - add option -deloutp (-do) to remove output file after successful run
3029 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
3030 extract exact list of procs from this file ; adjust COMMAND by
3031 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
3032 o pkg/ecco: replace old ineffective way of penalizing deviations from
3033 first guess (of obcs) with code by Matt Mazloff
3034 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
3035 exf/cal
3036 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
3037 and handle case of obcs?period == 0
3038 Not affected by these changes: There is still an inconsistency in
3039 the computation of start/endrec for the obcs variables for ALLOW_CAL
3040 defined (see comment by Menemenlis, 7-Mar-2003)
3041 - make S/R ctrl_get_gen_rec return something meaningful even if
3042 ALLOW_CAL is not defined
3043 - ctrl_getobcs?: simplify code so that it does not need to use
3044 S/R exf_swapfields
3045 o testreport:
3046 allow to test MPI with different number of processors for each experiment:
3047 create file "SIZE.h.mpi" in each build dir.
3048 Note: update of "-command" argument not yet implemented.
3049 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
3050 alleviate the need for additional 3D tapes when using
3051 the non-inear free surface in the adjoint. This is done
3052 by adding an 'update' of hfacc etc. to their current
3053 value at the beginning of forward_step.F.
3054 o pkg/seaice
3055 seaice_lsr: move stress-divergence computations out of outer pseudo-
3056 timestepping loop
3057 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
3058 up, so that the calls of the ctrl_* subroutines are really at the end
3059 of the routine.
3060 o pkg/gmredi:
3061 allow to specify a 2-D horizontal map and a 1-D vertical profil
3062 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
3063 o pkg/seaice:
3064 move lsr iterations from seaice_dynsolver to seaice_lsr.
3065 o pkg/seaice:
3066 reduce memory footprint of seaice mutldim advection tapes,
3067 by using a 2D tape independent of the generic_advdiff ones,
3068 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
3069
3070 checkpoint62q (2010/12/29)
3071 o model/src:
3072 - check horizontal grid-spacing for unset or zero/negative values.
3073 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
3074 o pkg/flt:
3075 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
3076 - precision of input and output files set according to readBinaryPrec
3077 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
3078 - initial float position from tiled file was not converted to index space
3079 (looks like a bug): fixed to make it similar to initial pos. global file.
3080 o global_ocean.cs32x15:
3081 change SIZE.h of AD set-up to get same tiling as with MPI.
3082 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
3083 o model/src:
3084 add flag to control printing of domain fields (bathymetry, hFac ...) in
3085 ini_mask_etc (call to plot_fieds_xy*).
3086 o pkg/thsice:
3087 if useEXF, some forcing fields are not valid in overlap: fixed by computing
3088 over the interior only + apply EXCH at the end (like with SEAICE advection).
3089 o pkg/mdsio:
3090 - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
3091 to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
3092 - change barrier call for safe multi-threads access to 3-D shared buffer.
3093 - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
3094 - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
3095 remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
3096 o pkg/flt:
3097 - add fourth-order Runge-Kutta integration
3098 - add basic exch2 support (only 1 facet supported so far!)
3099 o pkg/mdsio+rw:
3100 new S/R to read local (or tile independent) vector (read counterpart of
3101 mds_writevec_loc, and front-end write_glvec_rl/rs).
3102 o global_ocean.cs32x15: additional input_ad.seaice experiment
3103 that uses pkg/seaice rather than pkg/thsice.
3104 (using multidim advection for seaice)
3105 o towards more F95 syntax for array specification in namelist:
3106 - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
3107 of all verification experiments.
3108 e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
3109 was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
3110 - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
3111 o global_ocean.cs32x15: additional input.seaice experiment
3112 that uses pkg/seaice rather than pkg/thsice.
3113
3114 checkpoint62p (2010/12/17)
3115 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
3116 to THSICE_SIZE.h to avoid conflict with pkg/seaice.
3117 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
3118 allow for use of multim. advection in seaice adjoint.
3119 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
3120 - first attempt to close budgets by taking into account the freshwater
3121 flux implied by the sublimation of snow and ice. So far only the
3122 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
3123 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
3124 o eesupp/src:
3125 new S/R with new option (NML_EXTENDED_F77) to change array specification
3126 from F95 standard to commonly accepted extended F77 form.
3127 This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
3128 and to revert back to the original syntax (with -DNML_EXTENDED_F77)
3129 for less tolerant f77 compiler (e.g., pgf77, g77).
3130 o globalFiles:
3131 commented out in parameter file "data" since it's not safe with MPI
3132 (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
3133 in this case); no longer commented out in restart test (tst_2+2).
3134 o add adTapeDir to specify a special directory where adjoint tapes are
3135 written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
3136 and cannot be used together with mdsioLocalDir.
3137 o nesting pkgs:
3138 - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
3139 - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3140 - add parameter files + utils dir + output from short run on beagle.
3141 o pkg/seaice:
3142 fix seaice_growth.F store directives; update results of exp. lab_sea.ad
3143 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
3144 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
3145
3146 checkpoint62o (2010/11/25)
3147 o pkg/exf:
3148 - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
3149 o pkg/seaice:
3150 - seaice_ocean_stress: split a loop for better vectorization of the
3151 adjoint code
3152 - seaice_growth.F: fix bug in conservation of freshwater connected to
3153 capping of heff, put contribution into d_HEFFbyNEG
3154 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
3155 by something more sensible (parameters that are what their name implies)
3156 - change some defaults, so that by default exf-parameters are used for
3157 things like rhoAir, cpAir,latent/sensible heat parameters, in order
3158 to reproduce the old results, many data.seaice now contain funny values
3159 for cpAir and latent heat of sublimation
3160 o packages_readparms.F: move exf_readparms up in line so that
3161 exf-parameters are visible for other packages (e.g. seaice)
3162 o debugMode & debugLevel=2:
3163 - differentiate between debugMode & debugLevel=2:
3164 debugMode: controls printing of debug messages (sequence of S/R calls).
3165 debugLevel: controls printing of algorithm intermediate results and stats.
3166 - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
3167 => allows to print debug-stats without all sequence of call messages.
3168 - switch control of debug print from debugLevel to debugMode in many S/R.
3169 o pkg/obcs (obcs-sponge):
3170 fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
3171 call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
3172 o pkg/generic_advdiff:
3173 - record overlap minimum size for each advection scheme;
3174 - refine criteria on overlap minimum size;
3175 - check and stop (in gad_check) if overlap size is too small.
3176 o pkg/obcs:
3177 - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
3178 once, in ptracers_implicit.F)
3179 - with seaice: remove test on empty file name in obcs_apply_seaice (always
3180 apply OB values when tile has OB)
3181 o model/src, coriolis setting:
3182 - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
3183 useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
3184 files (selectCoriMap=3) with any grid.
3185 - add parameter "fPrime" for constant second Coriolis coeff (default=0).
3186 o pkg/seaice/seaice_growth.F:
3187 a few cosmetic changes that reduce the number of lines of code
3188 o pkg/obcs: add boundary conditions following Stevens (1990)
3189 - the code follows old MOM/NAOSIM code
3190 - so far it is only implemented for the eastern and western boundaries
3191 and NOT for pTracers
3192 o pkg/rbcs:
3193 - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
3194 beginning of the first rbcs forcing period.
3195 - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
3196 offline package, i.e., one file per time, labeled by iteration number;
3197 deltaTrbcs sets the timestep with which the data was generated;
3198 rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
3199 - rbcsForcingCycle=0 makes forcing non-cyclic.
3200 - make arithmetic safe for negative times and odd forcing periods.
3201
3202 checkpoint62n (2010/11/09)
3203 o pkg/seaice:
3204 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
3205 o pkg/obcs:
3206 New S/R to copy tracer value from the OB location to narrow band region
3207 (width = same as overlap) beyond the OB: preserve OB value (needed for
3208 high-order scheme) which were overwritten by EXCH call if in overlap
3209 region. Applied to theta, salt, ptracer and advected seaice variables.
3210 With seaice: use maskInC in similar way as in gad_advection.F,
3211 in seaice_advection.F and advect.F.
3212 Update output of experiment seaice_obcs and change exp4 to test OBCS with
3213 4th order Adv.Scheme. for pasive salt and ptracer.
3214 o tools/genmake2:
3215 - when looking for an optfile (not specified), only search for Fortran compiler
3216 (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
3217 - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
3218 (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
3219 - set default for CPP to "cpp -traditional -P" (was the case without specifying
3220 an optfile, but otherwise default was just "cpp".
3221 - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
3222 - when "CC" is not set in the optfile, look for possible C compiler
3223 (instead of just setting CC=cc)
3224 - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
3225 => add a ".F" to ".o" rule for source files with no "#include" (such as
3226 port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
3227 - move gfortran before g77 in list of possible Fortran compiler (consistent
3228 with reference compiler switch from g77 to gfortran)
3229 o pkg/seaice:
3230 o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
3231 seaice_check that stops the model, when the CPP flag is used.
3232 o seaice_growth.F: make capping of ice volume conserving by returning the
3233 capped ice as freshwater to EmPmR. This does not change the verification
3234 experiments but will change runs where the capping is acutally active
3235 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
3236 (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
3237 global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
3238 lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
3239 o tools/genmake2:
3240 - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
3241 - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
3242 - clean previous genmake log files before anything else.
3243 - change Makefile to remove testreport log files (*.tr_log) and genmake log
3244 files only with "CLEAN" target (instead of "Clean");
3245 o pkg/generic_advdiff:
3246 Change OBCS in multiDim advection (gad_advection.F):
3247 Use maskInC to prevent intermediate update of tracer-field in OB regions,
3248 thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
3249 which were applying future time-step OB values.
3250 This way, all explicit calculations use current-time-step OB values
3251 (simpler and more consistent).
3252 Affects results when set-up uses time-varying OBC and multi-dim advection;
3253 update output of experiment seaice_obcs.
3254 o pkg/seaice:
3255 move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
3256 this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
3257 SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
3258 Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
3259 but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
3260 unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
3261 o pkg aim (2010/10/26):
3262 - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
3263 formulation with obliquity, eccentricity, ... as run-time parameters,
3264 - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
3265 upward shortwave radition at the surface (all-sky and clear-sky).
3266 o pkg/obcs:
3267 - writing sections with globalFiles=T does not work: switch to tiled-files
3268 when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
3269 - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
3270 - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
3271
3272 checkpoint62m (2010/10/21)
3273 o pkg/seaice: vectorize seaice_solve4temp.F
3274 - move iterations loops outside of i/j-loops
3275 - requires 2D arrays for TB and effConduct
3276 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
3277 modified in this routine
3278 - a little bit of clean up, adjusting indentation, etc.
3279 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
3280 performance and '**TWO' by '**2' (because TWO is a float),
3281 replaced ONE, ZERO
3282 o eesupp/src:
3283 fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
3284 o pkg/seaice/seaice_growth.F
3285 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
3286 merging process. The merged routine has two branches, and one activates the 'evolution'
3287 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
3288 In summary, here is what the '10/10 revision' did consist of
3289 part 1: seaice_growth.F revisions 1.71 to 1.75
3290 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
3291 The emphasis here was on improving readability (e.g. by trying to use meaningful
3292 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
3293 part 1.5:
3294 - revising the lab_sea experiment to make it a more useful (i.e. stable
3295 and representative of an actual model run). This was done by generating a
3296 (winter) pickup to start from, switching back the main experiment dynamic
3297 solver from evp to lsr, having one of the experiments use the free drift solution.
3298 part 2: seaice_growth.F revisions 1.76 to 1.85
3299 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
3300 - Sorting out the various fields units and sign (set early on and reset at the end)
3301 to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
3302 fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
3303 - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
3304 and simplifying logical expressions to further improve readibility.
3305 part 3: seaice_growth.F revisions 1.86 to 1.89
3306 - Re-organize the blocks of code more logically.
3307 - Merging the '_if.F' pieces that add something new.
3308 o pkg/thsice:
3309 - vectorize thsice_solve4temp and thsice_get_exf.
3310 Problem: thsice_solve4temp has an unvectorizable statement that
3311 might also be problematic for TAF
3312 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
3313 does not change the verifcation experiment, but will change all
3314 experiments that have this flag undefined (not tested in verification);
3315 a little reorganization to save a few 2D fields and recomputations
3316 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
3317 - 2nd step: fix some store dirs
3318 o seems to work somewhat, i.e. using ifort but not g77
3319 o likely cause are incomplete init. or recomputation
3320 o start verification/global_ocean.cs32x15/input_ad.thsice
3321 o pkg/obcs: add support for exch2
3322 - the position of the boundary and prescribed values are specified using
3323 a global domain with exch2 facets stacked
3324 - in x for N,S boundaries (like W2_mapIO=-1)
3325 - in y for E,W boundaries (so E,W boundaries do not overlap)
3326 o pkg/mdsio: add support for writing global sections with exch2
3327 file layout is as for obcs described above:
3328 - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
3329 - for y-z sections, facets are stacked in y
3330 o pkg/thsice:
3331 - change a few routines for better vectorization: thsice_albedo.F,
3332 thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
3333 not affected, but in particular the latter routine has changed
3334 dramatically (not necessarily easier to read now).
3335 - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
3336 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
3337 o verification/lab_sea:
3338 - overhaul of the forward model experiments. The main motivation
3339 for this revision is that lab_sea has proven quite fragile (when
3340 changing the sea-ice code, and switching platforms) to a point
3341 when failures were very hard to attribute to specific code problems.
3342 - the suspected reason for this fragility is noise amplification by evp so,
3343 to start with, we decided to replace evp with lsr in the main experiment.
3344 - the input.lsr experiment thus became obsolete and was removed.
3345 - it was replaced with the input.fd experiment that uses an
3346 analytical "free drift" solution as the ice velocity field.
3347 - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
3348 will hopefully allow us to discriminate problems due to dynamic solvers
3349 from problems due to the thermodynamic code. input.salt_plume (lsr) allows
3350 us to test additional options, along with the salt plume package.
3351 - Finally a pickup was generated (at the end of a one year run) to
3352 make the tests more representative of an actual model run. Previously
3353 the tests starting point was a 1m thickness of ice everywhere.
3354 o pkg/seaice:
3355 - introducing S\R seaice_freedrift.F that compute the
3356 analytical solution to an approximate ice momentum
3357 equation (i.e. the simple stress/coriolis balance).
3358 - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
3359 of the free drift velocity field, and enable its use.
3360 To actually use the free drift solution as the model ice
3361 velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
3362 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
3363
3364 checkpoint62l (2010/10/04)
3365 o pkg/seaice:
3366 -fix the USE_ORIGINAL_SBI version (for variable freezing point);
3367 -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
3368 version (with USE_ORIGINAL_SBI undef);
3369 o add hooks for new packages OASIS, the package will follow
3370 (hooks exclude the seaice pkg for now)
3371 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
3372 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
3373 rather than mdsio_readvector.F/mdsio_writevector.F, within
3374 adread_adwrite.F to read/write adjoint-related tapes to disk.
3375 o eesupp and pkg/mdsio: ALLOW_WHIO
3376 Option to write/read 2D fields to files including tiles halos.
3377 The main purpose is for adjoint related "tape I/O".
3378 The secondary purpose is for debugging phases.
3379 A word on those rather specifically intended purposes.
3380 The code was meant to be stripped down to the bare minimum.
3381 Typically, there is a unique and basic mapping to the global
3382 buffer (tile by tile, then proc by proc, then level by level), and
3383 byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
3384 meant to generate user friendly outputs of various shapes and forms.
3385 Rather it is intended, for the knowledgeabale developers,
3386 to be largely independent of the many mdsio options, to allow
3387 outputs of tiles+halos in debugging phases and in adjoint runs,
3388 and to allow some flexibility in tuning (adoint) I/O depending on each
3389 file system behavior. With regard to tuning, most of the potential knobs
3390 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
3391 to specify directories, to specify the typical size of I/O calls, etc.)
3392 are not yet included, and will be added if they prove useful.
3393 o pkg/seaice:
3394 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
3395 o pkg/seaice:
3396 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
3397 code (seaice_budget_ice_if.F) which enable to recover old standard
3398 code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
3399 temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
3400 o model/src (rStar):
3401 use simple average (not area weighted) of rStarFac at U,V point when using
3402 vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
3403 update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
3404
3405 checkpoint62k (2010/09/17)
3406 o adjoint
3407 * changed verification/global_ocean.cs32x15 ; adjoint now tests
3408 Adams-Bashforth 3 + NLFS + RSTAR
3409 * some more modifs required for ECCO-GODAE v4
3410 o pkg/seaice
3411 add SEAICE_AGE_VOL option to use volume instead of area for
3412 integrating SEAICE_AGE
3413 o model/src:
3414 first check-in of sigma & hybrid-sigma coordinate code ; also includes
3415 non-linear free-surface parts ; but pressure-gradient not yet coded.
3416 o pkg/ptracers:
3417 option for ptracer to convert Salt Relax into additional EmP.
3418 tested in exp. global_ocean.90x40x15.dwnslp (update output)
3419
3420 checkpoint62j (2010/08/25)
3421 o pkg/ggl90:
3422 other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
3423 o pkg/dic: car_flux.F, phos_flux.F
3424 - reduce number of exp-calls in order to improve performance
3425 - clean up a little (replace fields by their macros, etc., fix
3426 typo in CPP-flag)
3427 o pkg/ggl90: minor changes
3428 - GGL90diffKrS was removed --> always use GGL90diffKr
3429 - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
3430 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
3431 (commented out for now)
3432 - change in max/min operations to ensure that smoothing is ok
3433 - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
3434 - always use diffKrNrT as background profile (i.e. never use diffKr field)
3435 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
3436 o pkg/dic:
3437 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
3438 vectorization
3439 - small bug fix in insol for the unlikely case of a cartesian grid
3440 - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
3441 + now vectorize, which also removes adjoint recomputations;
3442 + replace integer maksp1 by _RL maskp1
3443 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
3444
3445 checkpoint62i (2010/07/21)
3446 o pkg/flt:
3447 - with OBCS: stop floats which enter the OB region
3448 o model/src:
3449 - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
3450 for implicit vertical advection.
3451 o pkg/seaice:
3452 - account for melting in seaice age evolution.
3453 - remove double counting of seaice ridging effect on seaice age.
3454
3455 checkpoint62h (2010/06/18)
3456 o pkg/exch2:
3457 - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
3458 o tools/genmake2
3459 - remove "-pdefault" option: redundant with the use of "packages.conf";
3460 - remove file pkg/pkg_default : set the default as a pkg group
3461 ("default_pkg_list") defined in pkg/pkg_groups;
3462 - fix for case pkg/pkg_depend is missing (was hanging before);
3463 - add option "-pgroups" to specify a different pkg_groups than the default.
3464 o verification/adjustment.cs-32x32x1:
3465 add a "minimal" set-up test (code_min & input_min) which only compiles
3466 eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
3467 o tools/genmake2
3468 - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
3469 - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
3470 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
3471 files are nearly the same anyway.
3472 Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
3473 - redefinition of tau(i,i) (by a factor of ustar)
3474 - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
3475 - replace rhonil by rhoConstFresh in computation of evap (bug fix)
3476 - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
3477 - replace
3478 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
3479 shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
3480 by
3481 shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
3482 (changes results)
3483 -> exf_bulkformulae v1.22,
3484 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
3485 (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
3486 output.txt 1.63
3487 offline_exf_seaice: output.seaicetd.txt 1.7
3488 seaice_obcs: output.txt 1.10)
3489 Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
3490 -> exf_bulkformulae v1.23,
3491 unfortunately requires updating lab_sea.salt_plume (6 matching digits),
3492 and global_ocean.cs32x15.icedyn (only 11 matching digits)
3493 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
3494 o adjoint of exch-1:
3495 - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
3496 (note: was already like this when using EXCH-2) and remove flow dir
3497 and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
3498 - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
3499 - update pkg/exch2 diff list.
3500
3501 checkpoint62g (2010/05/19)
3502 o eesupp/src (exch-1):
3503 - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
3504 and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
3505 (renamed to exch1_*rx_cube.F).
3506 - change accordingly exch_*_rx.template and AD version in pkg/autodiff
3507 to call new exch1 S/R ; update Makefile and .cvsignore.
3508 - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
3509 exch2_xy_rx later)
3510 Note: after updating your code, need to run "make clean" in eesupp/src
3511 o test experiment bottom_ctrl_5x5:
3512 new output_adm.txt with fewer grdchk & less monitor output.
3513 o model/src:
3514 remove the call to ini_cori in initialise_varia.F (just keep the usual one
3515 in initialise_fixed.F). More consistent with coriolis & horizontal grid
3516 beeing treated in the same way (ini_grid is not called a 2nd time).
3517 o pkg/exf:
3518 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
3519 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
3520 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
3521 - cosmetic changes to exf_bulkformulae.F to make it look more like
3522 exf_bulk_largeyeager04.F
3523 o eesupp/src (exch-1):
3524 - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
3525 - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
3526 array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
3527 (even without using MPI).
3528 - Message mode: move RecvAck setting (indicator of buffer being ready)
3529 from send_put to recv_get S/R (was useless before, but not sure if
3530 it's much more useful now);
3531 - Switch the order of sync: MPI-proc 1rst and then threads;
3532 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
3533 - fix AD code for communication mode ='get' (but not used).
3534 o model/src:
3535 initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
3536 not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
3537 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
3538 o pkg/ctrl: require a specific set of control variables and exf-flags for
3539 adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
3540 o model/src:
3541 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
3542 1rst forward sweep, to avoid over-writing output files during recomputations
3543 recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
3544 b) 2nd version:
3545 - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
3546 - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
3547 writePickupAtEnd) + seaice & ptracers output;
3548 - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
3549 o model/src:
3550 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
3551 o pkg/exch2:
3552 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
3553 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
3554 o pkg/autodiff & exch2:
3555 process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
3556 (for now, only if ALLOW_EXCH2 is defined).
3557 o pkg/autodiff:
3558 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
3559 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
3560 + clean-up comments (_RS is not always real*4)
3561 - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
3562 - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
3563 was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
3564 o testreport (AD-tests):
3565 no longer link files from dir "../input" (1rst link files from
3566 "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
3567
3568 checkpoint62f (2010/04/29)
3569 o model/src/the_main_loop.F:
3570 adjust store directives for seaice evp and multicategory according to
3571 pkg/ecco/the_main_loop.F
3572 o adjoint:
3573 global_sum_ad was incomplete (noted many times by many people ;)
3574 nice description by Jean U. as follows:
3575 * allreduce(var) in global_sum.F can be interpreted as
3576 reduce(sum) followed by broadcast of sum.
3577 * The adjoint of that is
3578 sum(adjoint) followed by broadcast(summed adjoint value)
3579 or in other words, allreduce(sum, adjoint vars)
3580 We were missing the sum(adjoint)!
3581 Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
3582 (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
3583 The fix should produce 16-digit accuracy between
3584 single-CPU multi-tile (e.g. nSx=2, nPx=1) and
3585 multi-CPU single-tile (e.g. nSx=1, nPx-2)
3586 We'll probably change this yet again shortly
3587 o eesupp/src:
3588 - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
3589 o pkg/icefront
3590 - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
3591 specification of addmass array based on a 2D field, which is added
3592 at bottommost wet level at each horizontal location.
3593 o model/src:
3594 horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
3595 layout; (not always compatible with delX,delY setting; commented out for now).
3596 o pkg/exch2:
3597 change tile to processor setting (case nSy*nPy > 1): allows default model mapping
3598 (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
3599
3600 checkpoint62e (2010/04/15)
3601 o pkg/obcs:
3602 - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
3603 o pkg/dic:
3604 -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
3605 (note: not presently tested in any forward verification exp.)
3606 update tutorial_global_oce_biogeo AD output file.
3607 o pkg/exf:
3608 - account for the variation of albedo as a function of zenith angle
3609 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
3610 o build_options:
3611 - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
3612 o pkg/dic:
3613 change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
3614 - use binary pickup file for restart;
3615 - initialise atmos-CO2 box from dic_pCO2 parameter;
3616 - fix multi-threaded.
3617 o pkg/rbcs:
3618 - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
3619 change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
3620 - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
3621 and update output.txt
3622 o pkg/kpp:
3623 - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
3624 - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
3625 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
3626 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
3627 - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
3628 KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
3629 o pkg/offline:
3630 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
3631 (bug was added in version 1.10 on 2007-08-23).
3632 o pkg/offline:
3633 - no need to specify periodicExternalForcing, etc ... to use offline pack
3634 - offline input files no longer just single prec --> parameter offlineLoadPrec
3635 o verification/lab_sea:
3636 change AD test to multi-tile setup and update all 4 AD output.
3637 NOTE: while cost function values remain very similar,
3638 gradients are very different, although gradient checks are self-consistent
3639 Should try to get to the bottom of this (cost function summation order?)
3640 o pkg/dic:
3641 in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
3642 a weakness of TAF that drops part of double precision in log10 derivative.
3643 <= changes removed since problem has been fixed in current TAF version 1.9.71
3644 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
3645 o pkg/ecco:
3646 add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
3647 update all 4 lab_sea AD output.
3648
3649 checkpoint62d (2010/03/22)
3650 o build_options:
3651 remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
3652 o remove unbalanced quote (single or double) in commented line of source code
3653 (may cause some warning with some preprocessor/makedepend versions).
3654 o pkg/seaice:
3655 fix seaice_model.F for adjoint (gael) and update AD results of experiments
3656 lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
3657 o testreport:
3658 add option '-runonly' (short: '-ro') to just do the run part (without make).
3659 o eesupp: remove JAM communication code (obsolete).
3660 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
3661 (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
3662 to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
3663 (update also the output).
3664
3665 checkpoint62c (2010/03/02)
3666 o tools/build_options :
3667 move (some) old optfiles from build_options/ to build_options/unsupported/
3668 o model/src and pkg/exf
3669 surface relaxation -- separating data and data.exf options
3670 The point is to ensure that we specify the surface relaxation
3671 either in data or in data.exf (but not half and half) and to
3672 avoid an accidental relaxation to 0 (which happened if a time
3673 scale was specified but the file name was left empty)
3674 o model/src model/inc and pkg/mom_common
3675 ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
3676 => addition to the viscosity field as computed by others schemes
3677 o tools/build_options:
3678 - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
3679 but keep the former optfile for few weeks for smooth transition
3680 o pkg/ecco
3681 - allow user defined cost function contributions
3682 CPP: ALLOW_USERCOST_CONTRIBUTION
3683 USAGE: compute contributions in cost_usercost_all.F
3684 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
3685 the two options are complementary.
3686 o pkg/smooth
3687 - migration from contrib to the main repository
3688
3689 checkpoint62b (2010/01/26)
3690 o pkg/monitor:
3691 - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
3692 (in case someone forgot to update customized pieces of code)
3693 o nonHydrostatic:
3694 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
3695 - add a simple 2-D experiment (short_surf_wave) to test it.
3696 o pkg/icefront:
3697 adding the shell of, and the hooks to, a new package that
3698 will model melting and freezing of vertical glacier ice fronts
3699 o momentum:
3700 add diagnostics of momentum tendency from Hydrostatic pressure gradient
3701 (without surf.pressure term: would need a 2nd filling since implicit term).
3702 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
3703 two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
3704 cannot deal with the former
3705 o cleaning:
3706 - remove all (except OpenAD) old TLM output from results_ad dirs.
3707 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
3708 - comment out maskH definition (replaced by maskInC)
3709 o pkg/monitor:
3710 - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
3711 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
3712
3713 checkpoint62a (2010/01/15)
3714 o model/src:
3715 - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
3716 o pkg/diagnostics:
3717 - add optional level number diagnostics (i.e., level number to be define
3718 explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
3719 - strictly check for valid parser-code(10) ;
3720 - check if adding diag to the list from the right place.
3721 o pkg/longstep:
3722 - change parameters and fix tracer conservation with rstar/nonlinear free surface
3723 o diagnostics:
3724 - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
3725 S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
3726 o pkg/diagnostics:
3727 - Add option for writing vertical integral (sum of selected levels) of an output
3728 field instead of writing output field levels. Activate this option on a per
3729 output-file basis, by setting the 2nd character of fileflag to 'I'.
3730 - Add field-specific information relative to level integral in 3rd postion
3731 of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
3732 vertically (x level-thickness x hFac), "r"=same but without hFac.
3733 o do_the_model_io:
3734 - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
3735 in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
3736 writing pickups and stopping.
3737 o pkg/diagnostics (for now, only with mdsio):
3738 - write time information to meta file (and modify accordingly rdmds.m) :
3739 time-averaged diagnostics output: write starting and ending time of the
3740 time-averaging interval ; snap-shot diagnostics output remains unchanged;
3741 o pkg/timeave:
3742 - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
3743 always Nr), now assumed to be equal to number of levels of averaged field;
3744 only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
3745 o pkg/sbo:
3746 - fix ocean bottom pressure global-average & 2-D time-ave output (was
3747 neither initialised nor filled).
3748 - add starting iteration in suffix of global-average output file
3749 (to avoid over-writing the file after a restart)
3750 - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
3751 o time-average:
3752 - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
3753 (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
3754 ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
3755 this fix DIC_COST cumulative-time array (previously: bi,bj,k)
3756 - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
3757 - fix missing accumulation for pkg/opps.
3758 - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
3759 (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
3760 - fix initialisation of time-ave vars and do only full time-step increment
3761 (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
3762 o pkg/layers:
3763 - use standard RW pkg S/R to write the output
3764 and remove local write_fld version (which had a problem).
3765 - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
3766 - fix LAYERS_CALC argument list.
3767 o pkg/timeave:
3768 - store cumulative-time in a simple tiled array (drop the level index)
3769 - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
3770 o pkg/ocn,aim_compon_interf
3771 - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
3772
3773 checkpoint62 (2009/12/23)
3774 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
3775 (was not previously tested in any other exp.)
3776 o pkg/monitor:
3777 - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
3778 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
3779 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
3780 - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
3781 - change del2 calculation.
3782 - use interior masks (instead of maskH, <- to be remove).
3783 - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
3784 o mask & obcs:
3785 - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
3786 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
3787 (called after packages_init_fixed)
3788 o pkg/obcs:
3789 - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
3790 Fixes bug in obcs+exf with nSx*nSy.GT.1
3791 - fix multi-tile handling in obcs balance code
3792 o nonHydrostatic:
3793 - Implement AB-3 for non-hydrostatic vertical momentum ;
3794 (change ordering of var. stored in pickup file when using NH)
3795 - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
3796 - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
3797 (in prep. for new NH free surface form).
3798 o pkg/obcs:
3799 add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
3800 o model/src:
3801 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
3802
3803 checkpoint61z (2009/12/01)
3804 o nonHydrostatic:
3805 Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
3806 a spurious source of energy in simple baroclinic adjusment test case.
3807 Update all non-hydrostatic exp output.
3808 o model/src (3-d solver):
3809 Change again 3-D solver free-surface RHS term when exactConserv=T:
3810 simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
3811 (which was not the case with previous formulation).
3812 To recover previous version, just reset "oldFreeSurfTerm" to previous value.
3813 Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
3814 o nonHydrostatic:
3815 - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
3816 for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
3817 - change 3-D solver to work with r* (for now, only with linear free-surf.)
3818 - add few debug diagnostics (cg3d_x, residual)
3819 o model/src:
3820 fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
3821 update output of exp. global_ocean.cs32x15.viscA4
3822 o update output of exp. global_ocean.cs32x15.icedyn after removing
3823 #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
3824 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3825 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
3826 for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
3827 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
3828 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
3829 runtime flag useSRCGSolver. Modify verification experiment global_with_exf
3830 to test this code
3831 o pkg/cd_code:
3832 Change defaut D-grid time-stepping to get the same for D-grid momentum as for
3833 C-grid momentum. D-grid velocity used to be stepped forward in time with
3834 Adams-Bashforth only on surface pressure term. Tests show that using AB on
3835 D-grid coriolis term improves stability (as expected from CD-scheme paper).
3836 To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
3837 Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
3838 lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
3839 tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
3840 Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
3841 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
3842 o pkg/obcs:
3843 - fix bug in initialisation (broken since Oct 1rst modification)
3844 for useOBCSprescribe without useEXF.
3845
3846 checkpoint61y (2009/11/15)
3847 o pkg/seaice
3848 - change (once again) the discretization for the evp solver: rather than
3849 squaring the averages of strain rates, average the squares to give
3850 a better approximation to VP behavior (in simple test); this breaks
3851 verification experiments that use EVP (lab_sea and lab_sea.hb87)
3852 --> update outputs
3853 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
3854 to improve vectorization of adjoint code on TARGET_NEC_SX
3855 o verification/vermix:
3856 - change vermix to a more "classical" 1d column with high vertical
3857 resolution, seasonal heat flux forcing and constant wind forcing
3858 --> update outputs
3859 o pkg/seaice
3860 - fix diagnostics of principal stress components for EVP
3861 - add optional diagnostics of non-linear convergence for LSOR solver
3862 - make maximum zeta a runtime parameter
3863 o model/src (3-d solver):
3864 Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
3865 which consisted in removing the Surf. Non-Hydrostatic pressure from the
3866 whole column and adding it to Eta (inspired from Casualli, 1999):
3867 Only affects 3-D solver initial guess and only if using ExactConserv,
3868 but tests did show a degradation of solver convergence. For this reason,
3869 decide to disable this piece of code.
3870 to recover previous version, just set zeroPsNH = exactConserv (line 78).
3871 Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
3872 o pkg/ggl90:
3873 - fix previous modif (unfortunatly has not been documented here).
3874 o pkg/seaice/autodiff:
3875 - add CPP flag to include clipping of zeta in EVP code;
3876 although clipping of zeta is not necessary for EVP and not recommended
3877 it was done by default, now clipping is disabled by default
3878 - modify computation and store zetaC/Z in seaice_evp for TAF
3879 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
3880 - change seaice_calc_viscosities/strainrates for better
3881 vectorization after AD by TAF
3882 - rearrange common blocks in SEAICE.h once again for easier dumps of
3883 adjoint output, adjust adcommon.h and g_common.h
3884 - change flux form of default advection scheme for better vectorization
3885 of adjoint code
3886 - modify lab_sea/input.lsr to test the flux form of default advection
3887 scheme
3888 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
3889 transition in checkpoint61r)
3890
3891 checkpoint61x (2009/10/19)
3892 o adjoint: adding two new verification experiments
3893 * tutorial_global_biogeo: an online dic sensitivity experiment
3894 (work with G. Forget)
3895 * tutorial_dic_adjoffline: an offline dic sensitivity experiment
3896 (an update of the Dutkiewicz et al., 2006 paper)
3897 Both use the same CO2FLUX cost function, but different controls
3898 Gradient checks look good, but some recomp. could still be traightened out
3899 Should add xx_dic control variable to test at some point
3900 o model/src:
3901 add run-time parameters to check and/or mask initial Temp & Salt
3902 o pkg/ptracers:
3903 apply zonal filter (if used) to all passive tracers
3904
3905 checkpoint61w (2009/10/12)
3906 o adjoint:
3907 * update and finish work on adjoint of dic package (G. Forget)
3908 * start adjoint of offline package
3909 * bug fix for cube-sphere TLM code (active_file_g.F)
3910 o tutorial_global_oce_optim:
3911 now tested with 4 tiles (change data.grdchk and update output_adm.txt)
3912 and add SIZE.h_mpi for MPI testing
3913 o pkg autodiff
3914 - fix bug in autodiff_restore
3915 - make genmake2 remove comments and empty lines from ad_input_code.f in
3916 order to reduce file size (new script file remove_comments_sed)
3917 o allows to specify vertical profile of vertical viscosity (viscArNr)
3918 o pkg autodiff
3919 autodiff_ini_model_io: comment out writing of grid information to netcdf
3920 files, because at this time the grid fields are a bunch of zeros
3921 (this is analogous to ini_mnc_vars.F)
3922 o pkg seaice/autodiff:
3923 left-over from removing the 3-time-level fields:
3924 - small rearrangement of common blocks (SEAICE.h)
3925 - fix field declaration in order to get meaningful output in
3926 adseaice.*.nc (adcommon.h)
3927 o pkg obcs:
3928 - go through NH code only if nonHydrostatic=T
3929 - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
3930 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
3931 => Update output of experiment seaice_obcs
3932 - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
3933 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
3934 - fix restart for useOBCSprescribe + useEXF
3935 o pkg ctrl
3936 - make obcs as control parameter work also with useSingleCPUio
3937 - replace a few sny and snx by Ny and Nx to be consistent with
3938 ctrl_set_globfld_x/yz.F
3939 o pkg seaice
3940 - re-introduce global field frWtrAtm for the case of
3941 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
3942 - catch the case of an empty filename in seaice_cost_init_fixed.F
3943 o pkg ecco:
3944 - small bug fixes in the_main_loop
3945 . fix order of monitor arguments
3946 . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
3947 . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
3948 that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
3949 - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
3950 imbalance diagnostics for wmean_h/sflux = 0
3951 - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
3952 - catch the case of empty filenames in ecco_cost_init_fixed.F
3953 and ecco_readparms.F
3954 - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
3955 to make this statement meaningfull in ecco_cost_weights.F
3956 o pkg zonal_filt:
3957 - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
3958 - when using rStar, filter uVel*hFacW instead of uVel
3959 (tested without topography: fix a Pb of growing instability with NLFS)
3960 o pkg/aim/thsice:
3961 -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
3962 (works as SST restoring)
3963 o pkg/thsice:
3964 -add specific parameter for salt restoring in slab mixed-layer
3965 (by default equal to the temperature restoring)
3966
3967 checkpoint61v (2009/09/21)
3968 o pkg/kpp:
3969 -add double diffusive contributions as a hack, turned off by default
3970 for now, and the code can be excluded with a CPP-flag
3971 EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
3972 -add a verification experiments to "vermix" to test this code
3973 o pkg/mom_common:
3974 Move computation of length scales to mom_init_fixed.F (avoid recomputation
3975 at each time-steps*levels).
3976 o pkg/layers:
3977 Created a new package for computing volume fluxes in temperature or
3978 [not yet implemented] density layers, e.g. for calculating residual
3979 overturning circulations.
3980 o pkg/diagnostics:
3981 implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
3982 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
3983 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
3984 To avoid mixing type (RS/RL) of input/output array argument,
3985 replace single mixed-type array with a pair from each type (RS/RL).
3986 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
3987 is now implemented for all pkgs (previously only done for the main pickup)
3988
3989 checkpoint61u (2009/08/25)
3990 o pkg/obcs:
3991 - change OB?eta from _RS to _RL and put them into a separate commen block
3992 - add code to read OB?eta from a file via obcs_prescribe_read: the code
3993 compiles and does not destroy any other experiments, the data is read
3994 properly, but the code is not tested in actual applications
3995 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
3996 create a meaningful unit attribute for the time coordinate variable
3997 o pkg/ebm: add plenty of missing "_d 0" ;
3998 update results of experiment global_ocean_ebm (fwd + adjoint tests)
3999 Notes: several pieces of code only works for (very) specific set up
4000 (domain size, lat range, etc ...); should be documented & stop if one
4001 of those assumptions is not meet.
4002 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
4003 update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
4004 and offline_exf_seaice (seaicetd + adjoint).
4005 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
4006 update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
4007 seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
4008 o few changes to pass when compiling with strick checking of arguments
4009 across S/R (allow to find few bugs in S/R calls).
4010 o pkg/seaice:
4011 - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
4012 2d-fields, for slightly better performance
4013
4014 checkpoint61t (2009/07/22)
4015 o pkg/seaice:
4016 - remove unused variables in seaice_evp
4017 - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
4018 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
4019 named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
4020 each processor opens a different file (a fix from Matt).
4021 o cg2d:
4022 use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
4023 this reduces number of EXCH calls by 2 when using exch2.
4024 For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
4025 directives and missing simple EXCH (exch_s3d_rx) adjoint code.
4026 o pkg/thsice:
4027 add code for Near Infra-Red albedo (from Jeff)
4028 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
4029 o ini_model_io:
4030 move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
4031 MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
4032 to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
4033
4034 checkpoint61s (2009/06/30)
4035 o pkg/exch2 (exch2_rxN_cube*):
4036 remove last BARRIER (no need to synchronise after getting data from shared
4037 buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
4038 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
4039 and generate new output (for the 2 tests) using default rotationPeriod.
4040 o pkg/exch2:
4041 - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
4042 (was already the case with AUTODIFF_EXCH2 defined)
4043 - add bj in exch2 arrays and S/R.
4044 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
4045 MLAdjust to exch2 (identical results except with MPI -> truncation diff);
4046 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
4047 - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
4048 GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
4049 - verification experiment natl_box.longstep
4050 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
4051 allow different versions of ifort (8 or 9) and different versions
4052 of mpi (mpich or mpich2) to be used with the same optfile.
4053 requires to load a netcdf module and set MPI_INC_DIR (see comments inside
4054 optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
4055 o pkg/seaice:
4056 fix previous modif (3-level field removed) for old-pickup reading
4057
4058 checkpoint61r (2009/06/25)
4059 o pkg/seaice:
4060 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
4061 1. introduce fields for time step (N-1)
4062 2. do not use levels 2 and 3 anymore (but keep them)
4063 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
4064 includes changes to pkg/thsice/thsice_get_velocity.F,
4065 model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
4066 pkg/obcs/obcs_apply_uvice.F.
4067 - completely remove code for leap-frog time stepping for second order
4068 advection
4069 - adjusted adjoint accordingly;
4070 gradient checks have improved by an order of magnitude!
4071
4072 checkpoint61q (2009/06/22)
4073 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
4074 - the boundary conditions along open boundaries are unclear, because the
4075 associated masks are set to zero and are thus treated as closed when
4076 applying the slip-boundary conditions.
4077 - move initialisation of grid variables from seaice_init_varia to _fixed
4078 o adding doc/diags_changes.txt
4079 o model/src:
4080 do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
4081 to avoid "_diags" naming if no relation to pkg/diagnostics.
4082 ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
4083 file and only call PLOT_FIELD_XYZ if debugMode=T.
4084 remove few PLOT_FIELD_XY calls outside initialisation.
4085 remove few unnecessary BARRIER.
4086 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
4087 of salt_plume package in Southern Ocean
4088 o pkg/thsice:
4089 - fix hOceMxL in overlap (needed for sea-ice advection);
4090 update output of experiment global_ocean.cs32x15.icedyn.
4091 o pkg/seaice:
4092 - make the (placeholder-)tracer IceAge a little more meaningful
4093 by avoiding ridging of age due to convergent ice flow
4094 - add diagnostics for surface temperature, atmospheric and oceanic
4095 heat flux, and atmospheric and oceanic ice growth
4096
4097 checkpoint61p (2009/06/10)
4098 o eesupp (global_max & global_sum):
4099 - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
4100 - remove starting & endding barrier (no longer needed)
4101 o pkg/mdsio, writelocal:
4102 works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
4103 (remove the STOP): uses shared buffer IO to store data from all threads
4104 and then let master-thread write nThreads tiles.
4105 o pkg/mdsio (read/write field):
4106 - tiled IO done in 1 piece (all levels at a time);
4107 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
4108 - multi-threaded: allow to read/write local (non-shared) array
4109 (was already working with singleCpuIO ; now works also without);
4110 => no longer needs barrier call after reading a file (added inside
4111 mds_read/write field).
4112 - move barrier calls outside gather/scatter_2d to mds_read/write_field
4113 o pkg/obcs/exf
4114 - exf_getffieldrec.F: add a few ". _d 0" and
4115 add code to catch the case fldperiod = 0.
4116 - obcs_precribe_read.F: change if statements so that they match
4117 the variable type (_RL)
4118 - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
4119 exf_iprec) as part of namelist EXF_NML_01
4120 o pkg/mdsio:
4121 - read/write tiled (local) files: read/write 1-level tile chunk at a time
4122 (instead of segment of length sNx); expected to speed up tiled IO.
4123 o pkg/exch2:
4124 - take buffer copy from/to array out of S/R exch2_send/recv into new
4125 S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
4126 (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
4127 - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
4128 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
4129 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
4130 including Topology header file (and common blocks).
4131 - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
4132 remove 2nd exch call in exch2_s3d_rx (no longer needed).
4133 - document S/R arg. list (+ update some comments)
4134 o pkg/seaice:
4135 - added SEAICE_CLIM_AIR code, which permits modulation of surface air
4136 temperature and humidity over sea ice based on climatological values.
4137 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
4138 of LSR (this change is expected to change the results slightly because now
4139 it uses slightly difference moduli from the second last LSR solution, but
4140 that is more consistent with the stress computations; this part of the code
4141 is not tested in the verification experiments)
4142 - fix diagnostics for flux of ice in case of B-grid
4143 - turn strain rates eij and press into global fields within global
4144 common block in SEAICE.h for more straighforward diagnostics
4145 - fix diagnostics for principal stress components, press, zeta, eta
4146 to give something meaning full
4147 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
4148 new output (all 4 tests) using default rotationPeriod.
4149 o pkg KPP:
4150 - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
4151 - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
4152 and normal grid from 1 to Nr)
4153 o Fix computations of L4rdt in mom_calc_visc.F
4154 o eesupp:
4155 new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
4156 should be called before a "stop" if we know that all process are going
4157 to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
4158
4159 checkpoint61o (2009/05/26)
4160 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
4161 o model/src/ini_curvilinear_grid.F:
4162 compute angleSin/CosC when they are not read from a file
4163 o pkg/seaice:
4164 add pseudo time stepping for LSOR
4165 o pkg/exch2:
4166 temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
4167 o pkg/seaice:
4168 Adding separate sea ice albedo, drag coefficients, and HO in Southern
4169 Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
4170 o SingleCpuIO:
4171 fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
4172 o pkg/seaice:
4173 put exchanged variable in (local) common block for MPI+Multi-Threads
4174 to work (necessary with exch1, and for now with exch2 too).
4175 o verification: to get more experiments tested with mpi, mth and mpi+mth,
4176 change tiling of:
4177 aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
4178 hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
4179 update output of exp:
4180 exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
4181 tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
4182 + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
4183 (note: output.txt generated on faulks using only 1 tile)
4184 o eesupp & mdsio (SingleCpuIO):
4185 - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
4186 parameter "W2_useE2ioLayOut" (read from file "data.exch2").
4187 Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
4188 - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
4189 - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
4190 gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
4191 o pkg/exch2:
4192 - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
4193 read parameter file "data.exch2" if it exists; otherwise try default regular
4194 cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
4195 - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
4196 with new code (not to be used, just as a backup solution).
4197 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
4198 in utils/exch2/input.
4199
4200 checkpoint61n (2009/05/12)
4201 o eesupp & mdsio (SingleCpuIO):
4202 - move mapping to global io-buffer inside gather_2d/scater_2d: this save
4203 memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
4204 receive real*4 array (instead of real*8) to read/write 32.bit files.
4205 (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
4206 and remove new mapping S/R)
4207 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
4208 - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
4209 xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
4210 when using exch2. Add S/R to map global io-buffer to global model array.
4211 - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
4212
4213 checkpoint61m (2009/04/29)
4214 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
4215 and add 3 other S/R for other types (R4,R8,RS).
4216 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
4217 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
4218 - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
4219 - reduce number of macro definitions (keep only those which are used);
4220 can always call directly the corrresponding S/R if needed.
4221 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
4222 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
4223 Fixed wrong type of arg in:
4224 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
4225 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
4226 To fix: global_sum of var in common block is wrong (multi-threaded) in:
4227 dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
4228 To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
4229 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
4230 "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
4231 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
4232 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
4233 edges are closed (zero depth); might happen with "blank tiles";
4234 for now, disabled if using OBCS.
4235 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
4236 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
4237 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
4238 to reduce length of 1.D array print in STDOUT.
4239 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
4240 + use 48 tiles (16x8): this will allow to test "blank tiles".
4241 o start to test MPI + multi-threaded (change testreport to skip tests
4242 where number of tiles do not match).
4243 o genmake2: add option "-omp" to turn on Open-MP ;
4244 passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
4245 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
4246 and keep the original tile numbering. Note: compatible with old
4247 W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
4248
4249 checkpoint61l (2009/04/07)
4250 o Overlaps had been forgotten in calculating ijk keys : fixed
4251 o fix cyrus makedepend for gcc 4.4
4252 o experiment fizhi-cs-aqualev20:
4253 switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
4254 and generate new output. Note: new output is much closer to the old
4255 one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
4256 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
4257 o pkg/fizhi:
4258 - change to avoid indices going deliberately over array-bounds
4259 - remove unnecessary MPI stuff
4260 - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
4261 - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
4262 does not go over array-bounds and therefore returns reliable output.
4263 - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
4264 this S/R has 4 output arguments, which are used inside "get_alarm";
4265 when it is called with the same variable "ndum" in place of several
4266 output arguments, this produces weird side effect inside "get_alarm"
4267 (e.g., datein=dates(n) is overwritten by timein=times(n) since both
4268 datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
4269 address) and produces error.
4270 o tools/gemake2: (March 27-29 2009)
4271 with option "-mpi": link *_mpi files from "MODS" dir (this is what
4272 testreport does).
4273 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
4274 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
4275 update lab_sea.lsr & lab_sea.salt_plume results
4276 o pkg/seaice:
4277 Major overhaul of the LSOR solver: change discretization from original
4278 finite differences to finite volume. The old routine is still in the
4279 file seaice_lsr.F and can be turned on with the CPP-flag
4280 SEAICE_OLD_AND_BAD_DISCRETIZATION
4281 Along with this change, the discretization of the strain rates is changed.
4282 The same flag turns on the old discretization in seaice_calc_strainrates.F
4283 All verification experiments with seaice are affected (except for
4284 seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
4285 results by setting the above flag.
4286 Further changes involve changes in defaults:
4287 - ALLOW_FLOODING is defined and turned on by default
4288 - SEAICEadvSnow = .true. is now the default
4289 - SEAICEadvSalt = .true. is now the default
4290 - SEAICEadvAge = .true. is now the default
4291 - SEAICE_clipVelocities = .false. is now the default
4292 (as per J. Zhang's recommendation)
4293 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
4294 is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
4295 - seaice_growth: replace computation of UG by a simple copy from wspeed
4296
4297 checkpoint61k (2009/03/18)
4298 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
4299 seaice_lsr: fixed a few metric terms,
4300 affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
4301 add more debugging diagnostics
4302 seaice_evp: removed superfluous many metric terms of FV discretization
4303 of stress divergence
4304 affects lab_sea, lab_sea.hb87
4305 seaice_ocean_stress: removed superfluous many metric terms of FV discretization
4306 of stress divergence for non-evp solver
4307 (this part is not tested anywhere)
4308 seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
4309 they were effectively only half slip
4310 affects lab_sea.hb87
4311 updated all relevant verification experiments (except lab_sea//output_adm.txt
4312 which was left over, but fails at level 7 & 6)
4313
4314 checkpoint61j (2009/03/17)
4315 o pkg/seaice: turn a few hard wired parameters into run time parameters
4316 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
4317 time in seconds as promised by the usints in seaice_monitor and exf_monitor
4318 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
4319 that are not cubed-sphere grids
4320 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
4321 o pkg/ctrl:
4322 fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
4323 o non-hydrostatic (calc_gw.F):
4324 fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
4325 update output of exp. global_ocean.cs32x15.viscA4
4326 o remove backward compatibility for thetaMin,phiMin
4327 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
4328 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
4329 interpolated wind field not only for curvilineargrid=.true., but also
4330 for a rotated grid (rotateGrid=.true.)
4331 o pkg/exf: add capability to bypass interpolation for runoff
4332 by setting yet another CPP-flag
4333 o eesupp/src, B-grid exchange:
4334 add simple (6 tiles, non MPI) CS exch + standard interface S/R.
4335 o autodiff
4336 new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
4337 allows to switch to single-prec common blocks;
4338 corresponding switch occurs in tamc.h, integer isbyte
4339 TAF store directivs "byte" and "kind" seem equivalent;
4340 Most tamc.h have been updated correspondingly.
4341
4342 checkpoint61i (2009/02/13)
4343 o autodiff:
4344 fix autodiff_sore/_restore indices for obcs
4345 (spotted by I. Hoteit, M. Mazloff)
4346 o pkg/autodiff, pkg/ctrl:
4347 Add flag to reduce all tapelev I/O to single-prec.
4348 In data.ctrl set
4349 doSinglePrecTapelev = .TRUE.
4350 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
4351 check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
4352 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
4353 real fresh water flux (not yet)
4354 o pkg/mdsio & rw:
4355 - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
4356 - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
4357 o pkg/flt:
4358 - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
4359 init_fixed & ini_varia.
4360 - clean-up & simplify linear interpolation S/R:
4361 move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
4362 - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
4363 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
4364 - add vert. coordinate & horiz. indices to output files.
4365 - change vertical position in initial condition, from index to depth [m].
4366 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
4367 (easier to get to a curvilinear grid) ; delX,delY no longer used.
4368 o pkg/ggl90: a few modifications:
4369 - fix bottom boundary condition, and interpolation of KappaE
4370 near top and bottom
4371 - use same set of viscosity/diffusivity for TKE/momnetum/tracer
4372 - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
4373 - add a few options for mixing-length upper limit (--> mxlMaxFlag)
4374 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
4375 (maintain temporary backward compatibility, until next checkpoint)
4376
4377 checkpoint61h (2009/01/27)
4378 o pkg/diagnostics with "periodic averaging diagnostics":
4379 fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
4380 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
4381 o pkg/obcs: fix loop ranges for balancing code
4382 o pkg/flt:
4383 - improve criteria for finding which tile owns a float.
4384 - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
4385 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
4386 aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
4387 with ocean biogeo)
4388 o pkg/flt:
4389 - do some cleaning and fix the restart ;
4390 - add output.txt in flt_example/results to get this pkg tested.
4391 o genmake2: add an EXTENDED_SRC option and flag.
4392 for now, cannot be turned on on command line (only through genmake_local)
4393 o pkg/mdsio: read/write vector:
4394 - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
4395 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
4396 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
4397 - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
4398 (drop to 4 digits matching for grad). But this test does not look very
4399 reliable (was already failling on eddy, fc5, at 6.digits). Update output.
4400
4401 checkpoint61g (2008/12/29)
4402 o pkg/flt:
4403 - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
4404 + make OPTIONS file more standard.
4405 - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
4406 - fix _BYTESWAPIO CPP-Flag
4407 - standard reading of file-parameter "data.flt"
4408 - fix argument list of S/R FLT_RESTART
4409 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
4410 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
4411 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
4412 a still unfixed compiler/optimization bug
4413
4414 checkpoint61f (2008/11/21)
4415 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
4416 update results of global_ocean.cs32x15.icedyn test.
4417 o move getcon.F from model/src to pkg/fizhi.
4418 o pkg/exf: add parameter for extrapolation of temp up to the surface
4419 and option to prevent negative evap (in bulk_largeyeager04 only).
4420 o Prather Advection scheme: fix tracer conservation for divergent flow
4421 (e.g., when using NonLin Free-Surface).
4422 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
4423 o gmredi (Visbeck-variable-K):
4424 - add more parameters to Visbeck-variable-K.
4425 - use a 5 points average for dSigmaR in Visbeck-K calculation
4426 (more "homogenous": same stencil and same weights as in dSigmaH)
4427 - update output of ideal_2D_oce experiment.
4428 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
4429 (#undef REAL4_IS_SLOW)
4430 - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
4431 coordinate variable
4432 - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
4433 (surface forcing fields), removes some of the functionality
4434 - model/src/write_grid.F: write _RS variables as RS-netcdf variables
4435 - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
4436 probably not all: copy _RS surface flux fields to RL field before
4437 calling DIAGNOSTICS_FILL
4438 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
4439 real*4 (CALL EXCH_*_RS) versions.
4440 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
4441 (generate new output).
4442
4443 checkpoint61e (2008/10/23)
4444 o gmredi (Visbeck-variable-K):
4445 - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
4446 - change computation of Visbeck-K where Slope > Smax :
4447 now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
4448 previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
4449 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
4450 to be the same as with Z-coord. (i.e., m/s & no-units respectively).
4451 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
4452 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
4453 does not become too large (to avoid precision problems in implicit-diffusion
4454 solver); update ideal_2D_oce output.
4455 o pkg ggl90:
4456 - in ggl90_cal.F: compute only one set of visc/diff, used to
4457 step forward TKE/T/S/momentum
4458 - default value of GGL90viscMax/GGL90diffMax larger and equal (to
4459 have Prandlt =1)
4460 o gmredi (fm07):
4461 - add lower limit on Transition layer thickness + lower limit on 1/lambda
4462 - allow to set few more params from data.gmredi
4463 o pkg ggl90:
4464 - add missing sqrt(2) factor in computation of mixing length
4465 scale in ggl90_calc.F
4466 (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
4467
4468 checkpoint61d (2008/09/25)
4469 o adjoint modifs
4470 - adapt to new field rhoInSitu
4471 - allow to revert from StoreDynVars2D, StoreDynVars3D
4472 to individual fields
4473 (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
4474 o store 3-D (in-situ) density in commom block (DYNVARS.h)
4475 - save 1 rho computation.
4476 - no longer modify T & S inland when using down_slope pkg.
4477 o gad_som : allow to switch to SOM advection for T & S without corresponding
4478 pickup files (using new S/R: MDS_CHECK4FILE).
4479 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
4480 (for useSingleCpuIO to work in multi-threaded)
4481 o pkg/shelfice:
4482 - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
4483 with SHELFICEtopoFile in data.shelfice
4484 - move code for reading ice shelf topography and modifying hFacC into separate
4485 subroutines of the shelfice package
4486 - separate initialisation of "fixed" and "variable" variables
4487 - kTopC is not (yet) replaced by kSurfC, although this is possible
4488 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
4489 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
4490 and rename:
4491 ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
4492 ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
4493 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
4494
4495 checkpoint61c (2008/08/30)
4496 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
4497 to add mass source/sink of fluid in the interior (3-D generalisation
4498 of oceanic real-fresh water flux).
4499 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
4500 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
4501 o new pkg: down_slope
4502 density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
4503 - presently, modify T & S inland (dwnslp_calc_rho.F).
4504 can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
4505 - implementation for ocean in P-coords not tested.
4506 - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
4507 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
4508 (to facilitate conversion of oceanic pkg to p-coordinate).
4509 o change FIND_RHO to FIND_RHO_2D :
4510 pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
4511 o new pkg: cheapaml
4512
4513 checkpoint61b (2008/08/05)
4514 o exch2:
4515 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
4516 - no longer depend on the order sequence (N,S,E,W).
4517 - 3rd exchange no longer needed (tested with 24 tiles).
4518 - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
4519 - exch_UV_A-grid readily available (but not yet tested).
4520 comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
4521 (both are no longer needed) in exch_uv: no effect in forward run; but
4522 get truncation error differences with adjoint exch.
4523 o exch2:
4524 - change index-bounds storage (moved from target to local tile,
4525 more intuitive this way) ; rename/remove some variables.
4526 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
4527
4528 checkpoint61a (2008/07/29)
4529 o exch2/matlab-topology-generator:
4530 fix bug in index bounds for N-S internal exchange (hard to tell if this
4531 had any effect on the solution).
4532 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
4533 is exceeded
4534 o testreport: modify syntax of awk, so that it works also with
4535 awk, and not only with nawk and gawk
4536
4537 checkpoint61 (2008/06/24)
4538 o autodiff
4539 Change default for TAF usage by removing argument '-nonew_arg'
4540 This changes TAF subroutine argument list (ordering of active var.)
4541 Omission of this flag leads to incompatibility w.r.t. TAMC
4542 To restore TAMC-compatibility, need following modifs:
4543 * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
4544 * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
4545 Tested TAF version is 1.9.22
4546 N.B.: exch2 hand-written adjoint code currently not TAMC compatible
4547
4548 checkpoint60 (2008/06/19)
4549 --->>> This is the last checkpoint for which generating the adjoint
4550 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
4551 --->>> by default.
4552 --->>> Future checkpoints will ommit this flag by default.
4553 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
4554 o pkg/grdchk: Add gradient check to etan0 perturbations.
4555 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
4556 o pkg/autodiff: more flexibility in zeroadj.
4557 model/src: modifying do_oceanic_phys.F accordingly.
4558 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
4559 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
4560 special setup of gmredi for which the adjoint is stable
4561 enough for parameter optimization.
4562 o bridging the gap between eddy stress and GM.
4563 -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
4564 along with a change in CPP option (now ALLOW_EDDYPSI).
4565 -> when using GM w/ GM_AdvForm:
4566 The total eddy streamfunction (Psi = eddyPsi + K x Slope)
4567 is applied either in the tracer Eq. or in momentum Eq.
4568 depending on data.gmredi (intro. GM_InMomAsStress).
4569 -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
4570 The key modifications are in model/src/taueddy_external_forcing.F
4571 pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
4572
4573 checkpoint59r (2008/05/29)
4574 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
4575 from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
4576 fix option to read coriolis(@ cell-corner) from files with CS-grid.
4577 o pkg/mnc: add some attributes to standard 1D-coordinate variables
4578 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
4579 mass points, when using mnc for output
4580 - add runtime parameter (missing_value, missing_value_int) to override
4581 default (which is the value of getcon('UNDEF'))
4582 o pkg/mnc: prepare mnc for the actual use of missing values with the
4583 diagnostics package: small fix in mnc_cw_readwrite.template and more
4584 initialisation of never used fields
4585 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
4586 versions
4587 o pkg/thsice/thsice_ini_vars.F added default initial values so that
4588 thermodynamics sea ice solver does not blow up when some initial fields
4589 are missing.
4590 o move from external_forcing_surf.F to ini_forcing.F
4591 the p-coord. hack consisting in using pLoad to set phi0surf ;
4592 update output of tutorial_global_oce_in_p (affected @ truncation level).
4593 o Freshen up a bit hs94.1x64x5, notably:
4594 remove rotationPeriod and tRef=5*0. (adjoint only), and add
4595 exactConserv=.TRUE.
4596 o pkg/generic_advdiff:
4597 change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
4598 applies to files where Temperature & Salinity 2nd Order moments are used.
4599 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
4600 this uses a dynamically allocated internal state data structure
4601 (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
4602 and requires a fortran 90 compiler
4603
4604 checkpoint59q (2008/05/06)
4605 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
4606 (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
4607 o Refresh tutorial_global_oce_biogeo, notably:
4608 - change bathymetry (put back seamounts in ACC, use hFacs)
4609 - change EOS (POLY3 --> JMD95Z)
4610 - use Bryan-Lewis vertical diffusivity
4611 - use multidimensional advection
4612 - remove old virtual virtual in dic pkg, now done through ptracer pkg
4613 - change a couple of parameters in dic pkg
4614 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
4615 o pkg/obcs: change default to OBCSfixTopo = .true.,
4616 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
4617 - replace "debugMode" with "debugLevel .GE. debLevB"
4618 o implementation of TAF directives for gchem,cfc,dic
4619 o remove "exp5" (replaced by tutorial_deep_convection).
4620 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
4621 this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
4622 the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
4623 --> changes results in exp4, seaice_obcs
4624 o tutorial_deep_convection :
4625 update the set-up and increase resolution and domain size ; start
4626 from pseudo initial conditions = output at t=120mn in order to see
4627 something happening when running testreport.
4628 o pkg/seaice: add os7mp as an advection scheme
4629 add check for advection schemes
4630 add a flag for restoring T and S underneath sea ice
4631 o pkg/my82: add netcdf-support and diagnostics
4632 o thsice pkg:
4633 - Now hsMax limits snow height by turning it into ice following
4634 flooding scheme (and now conserving energy)
4635 - Slight rewriting of the formula in thsice_calc_thick.F
4636 - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
4637 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
4638
4639 checkpoint59p (2008/04/10)
4640 o gchem / dic / cfc :
4641 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
4642 - add new parameter files: "data.dic" & "data.cfc" ;
4643 - various re-arrangement in initialisation & header file ;
4644 - fix tutorial_global_oce_biogeo for multi-threaded test.
4645 o pkg/dic: test for "pickup_dic" file when restarting ;
4646 if no pickup-file, can restart with a re-initialised pH (same as it did
4647 before) providing pickupStrictlyMatch is set to False.
4648 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
4649 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
4650 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
4651 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
4652 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
4653 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
4654 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
4655 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
4656 scheme to use for vorticty-term ;
4657 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
4658 (with default selectVortScheme, return to original discretisation)
4659 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
4660 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
4661 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
4662 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
4663 also fix diagnostics VISCAHW & VISCA4W.
4664
4665 checkpoint59o (2008/03/07)
4666 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
4667 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
4668 move a few statemens out the main loop into separate loops
4669 o pkg/shelfice:
4670 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
4671 (kg/m^2/s), does not break tests, because in verification/isomip,
4672 rhoConstFresh=rhoConst (by accident)
4673 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
4674 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
4675 new file model/src/seawater.F, so that they are available for all pkgs.
4676 - convert potential temperature into in-situ temperature. This changes the
4677 isomip tests => update tests
4678 o add a flag writePickupAtEnd (default=true) to be able to suppress
4679 writing a pickup at the last timestep
4680 o tools/mpack-1.6 :
4681 - disable automake (not working) and autoconf (not needed).
4682 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
4683 also cleaner with much less compilation warnings.
4684 o pkg/profiles:
4685 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
4686 (for "less than 32 characters name" compiler requirement)
4687 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
4688 conditions that have a different sampling frequency than S/T/U/V obcs
4689 o pkg/diagnostics (stats-diags):
4690 - fix global Min/Max in case 1 processor get only empty tiles
4691 o genmake2: replace (4 times)
4692 make genmake_tc_1.o >> genmake_warnings 2>&1
4693 with
4694 COMM="$CC $CFLAGS -c genmake_tc_1.c"
4695 echo $COMM >> genmake_warnings
4696 $COMM >> genmake_warnings 2>&1
4697 to make genmake2 always see the value of CC as specified in the optfile.
4698 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
4699 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
4700 - modify verification advect_cs test to test SOM-advection on CS-grid.
4701 o pkg/ctrl:
4702 - Rewrite of ctrl_map_ini_ecco.F,
4703 introducing a generic routine (ctrl_map_ini_gen.F).
4704 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
4705
4706 checkpoint59n (2008/02/09)
4707 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
4708 number in dedicate array "hdiag":
4709 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
4710 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
4711 - many small changes (integer format) for large number of diagnostics
4712 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
4713 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
4714 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
4715 usingSphericalGrid, this allows to define the rotated grid coordinates
4716 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
4717 geographical coordinates according to the inverse of the rotation defined
4718 by the Euler angles, so that Coriolis parameter and online-interpolation by
4719 exf works with the geographical coordinates on XC/YC/XG/YG.
4720 Naturally, this feature does not work with all packages, so some
4721 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
4722 profiles), because there the coordinates are assumed to be regular
4723 spherical grid coordinates.
4724 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
4725 - introduce isopycnal diffusion coefficient control.
4726 o tools/adjoint_options:
4727 - additional control vector components.
4728 o pkg/mnc: have mnc create marginally meaning full coordinate variables
4729 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
4730 o pkg/mypackage:
4731 - add example of read/write pickup for state-var ;
4732 - add entry points to the main code for state-vars diags & write-pickup.
4733 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
4734 transitions for useExfYearlyFields
4735 - add new subroutine that determines the file to read from for
4736 use*YearlyFields = .TRUE. and .FALSE.
4737 - add a verification experiment to global_with_exf that tests
4738 useExfYearlyFields with USE_EXF_INTERPOLATION defined
4739 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
4740 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
4741 subroutines (which could be generated from a template, because they are
4742 almost identical), for now they are included in obcs_prescribe_read.F for
4743 simplicity
4744 o pkg/exf:
4745 - add a little more diagnostic to exf_interp_read (in analogy to
4746 mds_read_field, can be turned off with debugLevel < debugLevA=1)
4747 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
4748 ugly but fast by unrolling short inner loops, inserting a unroll=8
4749 directive in routine lagran, and splitting a loop and making do while the
4750 outermost loop (the latter requires the intoduction of index arrays)
4751 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
4752 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
4753 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
4754 o verification/seaice_obcs: updated for restart test and latest options
4755 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
4756 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
4757 for now this is only available for the C-grid code and also within
4758 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
4759
4760 checkpoint59m (2008/01/14)
4761 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
4762 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
4763 o gad_som : fix flux output (& diagnostics) to have same units as other
4764 advection scheme fluxes (was previously multiplied by deltaT).
4765 o added verification/seaice_obcs both to test seaice open boundaries
4766 and to provide an example matlab scrpt for generating them
4767 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
4768 o pkg/salt_plume: clean up salt_plume_frac.F to
4769 remove redundancy in PlumeMethod 1 and 4
4770 o pkg/kpp: added saltplume diagnostics
4771 o pkg/obcs and pkg/seaice:
4772 - do not set uice and vice to zero when OB*icefile are unspecified
4773 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
4774 - moved seaice tracer obcs after call to seaice_growth
4775 o pkg/salt_plume: added various options for salt plume depth
4776 criterion and for vertical distribution of the salt
4777
4778 checkpoint59l (2007/12/18)
4779 o pkg/ptracers: new version of ptracers pickup:
4780 read meta file and write only fields which are needed to restart.
4781 ( same logic as main pickup file ; also using pickupStrictlyMatch )
4782 o pkg/seaice:
4783 - add timescale for melting due to warm mixed layer as a means of
4784 setting SEAICE_availHeatFrac more conveniently
4785 - add a CPP-flag/runtime parameter check for flooding algorithm
4786 - reformulated availHeat in seaice_growth.F to be independent of AREA
4787 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
4788 unit changes
4789 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
4790 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
4791 SX vector computer.
4792 o pkg/seaice:
4793 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
4794 seaice forcing fields can now be read only through pkg/exf
4795 - removed some unused halos
4796 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
4797 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
4798 or U/VICE from U/VWIND before computing U/VSTRESS
4799
4800 checkpoint59k (2007/11/30)
4801 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
4802 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
4803 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
4804 all experiments pass when compile with un-initialised var. checking option.
4805 o added pkg/salt_plume
4806 o script to test restart (for now, in MITgcm_contrib/jmc_script)
4807 o pkg/seaice: new read/write pickup version.
4808 read meta file and write only fields which are needed to restart.
4809 ( same logic as main pickup file ; also using pickupStrictlyMatch )
4810 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
4811 o lab_sea.hb87: modify the domain & update output.hb87.txt :
4812 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
4813 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
4814 process. Fixed here by closing the domain at the Northern boundary.
4815 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
4816 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
4817 a set of consecutive levels in/from a 3-D array.
4818 o pkg/ptracers:
4819 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
4820 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
4821
4822 checkpoint59j (2007/11/09)
4823 o in pkgs: dic, obcs, offline, rbcs:
4824 standard way to compute coeff. for time interpolation between 2 time reccords
4825 which retains full precision (& make results less dependent on compiler).
4826 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
4827 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
4828 packages instead of reading ice cover and wind speed separately
4829 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
4830 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
4831 to allow to compile customized code before the update)
4832 o cleaning-up:
4833 - fix CPP instruction syntax in pkg/obcs
4834 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
4835 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
4836 - fix some threads issue in IO parts.
4837 o pkg/dic:
4838 - add tons of "_d 0" (--> much better testreports !)
4839 and then update outputs of tutorial_global_oce_biogeo
4840 o pkg/mom_fluxform:
4841 add a special version of momentum advection intended to conserve momentum
4842 next to a bathymetry step or a coastline edge. (default = off = #undef)
4843 o new read/write pickup version:
4844 - for now, only implemented for main (mdsio) pickup file.
4845 - write out only what is needed to restart; merge pickup_nh , pickup_ph
4846 and main pickup together.
4847 - read meta file; read only what is needed to restart; stop if a field
4848 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
4849 if it make sense (even if the restart is not perfect).
4850 - if no meta file, assume that pickup to read corresponds exactly to
4851 a pickup that would currently be written.
4852 - read pickup written in the old format (until checkpoint59i) if it
4853 recognizes an old meta file (no field-list).
4854 - add a meta file in exp. which starts from a pickup: 2 cases:
4855 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
4856 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
4857 b) a meta file describing the content of the associated pickup file
4858 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
4859 o pkg/mdsio & pkg/rw:
4860 - new routine to read a meta file ; new set of routine to read
4861 Multiple-fields file (with meta file).
4862 o added open boundary conditions capability for seaice
4863 HSNOW, HSALT, UICE, and VICE
4864
4865 checkpoint59i (2007/10/21)
4866 o adjoint:
4867 * fix multiDimAdvection adjoint
4868 (partial recomputation problem by TAF for fVerT(:,:,kDown)
4869 and comlev1 size definition (maxpass vs. max. number of tracers)
4870 * verification/global_ocean.90x45x15 adjoint now tests
4871 NLFS and multiDimAdvection using DST3 (=30)
4872 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
4873 o pkg/kpp: add "_d 0" to real constant (if missing);
4874 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
4875 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
4876 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
4877 for internal parameters related to restart process (formerly from PARAMS.h)
4878 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
4879 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
4880 as argument. (only atm2d & obcs write_pickup have not yet been updated)
4881 o pkg/monitor:
4882 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
4883 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
4884 - account for deep Atmosphere factor and density factor (anelastic)
4885 o added open boundary conditions capability for seaice HEFF and AREA
4886 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
4887 thermodynamics
4888 - requires a little reorganization, which affects the testreport results
4889 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
4890 so that now the conservative form is tested
4891 - add a few comments
4892 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
4893 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
4894 o add new diagnostics to seaice: advective, diffusive fluxes (only for
4895 multidim-advection, for scheme 2 they are not filled) and transports,
4896 thermodynamic growth rates
4897 o change units of EmPmR (inside the code, + within coupling interface)
4898 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
4899 Affects results @ truncation level (cg2d match) and update output of
4900 experiments: lab_sea(6), global_ocean.90x40x15(10),
4901 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
4902 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
4903 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
4904 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
4905
4906 checkpoint59h (2007/09/29)
4907 o pkg/exf:
4908 - improve vectorization by moving if-statement out of loops in
4909 exf_mapfields, exf_radiation
4910 - exf_bulkformulae.F: introduce 2D fields and vectorize code
4911 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
4912 o testreport:
4913 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
4914 monitor & update offline_exf_seaice exp. output.
4915 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
4916 o pkg/seaice:
4917 - bug fix in the evp solver: boundary conditions were affected be
4918 masking of zMax/zMin (changes results)
4919 - minor bug fix in boundary conditions in seaice_calc_strainrates
4920 (changes results for no_slip)
4921 - seaice_lsr.F: make interpolation of eta dependent on boundaries
4922 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
4923 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
4924 stress formulation and no-slip boundary conditions
4925 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
4926 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
4927 o pkg/seaice: a first HSALT time stepping equation has been checked in
4928 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
4929 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
4930 without requiring DO-IF statements
4931 o pkg/thsice:
4932 use continuous power-law function for partition of energy between lateral
4933 melting/freezing and thinning/thickening ; old code using step function
4934 still available with #undef THSICE_FRACEN_POWERLAW
4935 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
4936 o testreport: change AD testing : check against results/output_adm.txt
4937 using same scripts as for forward test.
4938
4939 checkpoint59g (2007/09/17)
4940 o adjoint testing: in preparation for changing testreport:
4941 - output format: cost and grad written on separated lines
4942 - ad output results in directory "results" (instead of "results_ad")
4943 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
4944 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
4945 o pkg/ecco: allow user defined cost function contributions
4946 o testreport:
4947 Allow to choose (per experiment) the list of tested output variables
4948 and the main variable (used to issue a pass/FAIL ) ;
4949 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
4950 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
4951 Also modify printing of summary:
4952 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
4953 b) echo the list of tested variables in the individual summary.txt of
4954 each experiment.
4955 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
4956 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
4957 (but still depend on the tile decompostion of the domain).
4958 o pkg/seaice: change a discretization detail to make the B-grid code
4959 "more symmetric". This change is likely to remove all "ridges/leads" that
4960 where quasi-aligned with the grid in B-grid solutions. It may also be
4961 the solution to the stress coupling issues with the B-grid.
4962 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
4963 remove .cvsignore from input dir. (since testreport no longer run here).
4964 o pkg/thsice:
4965 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
4966 - fix reshaping of sea-ice just after advection:
4967 melt all the ice only if ice-volume is too small.
4968 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
4969 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
4970 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
4971 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
4972 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
4973 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
4974 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
4975 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
4976 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
4977 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
4978 -> update output.txt
4979 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
4980 this affects truncation error: -> update output.txt of exp:
4981 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
4982 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
4983
4984 checkpoint59f (2007/08/21)
4985 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
4986 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
4987 a bounded range (in forward mode)
4988 o pkg/ecco, ctrl, autodiff and mom_common:
4989 internal parameter controls, completements of implementations
4990 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
4991 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
4992 (not seem any difference in testing results).
4993 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
4994 at face corners.
4995 o pkg/generic_advdiff:
4996 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
4997 loop range indices for computing vertical advection tendency
4998 and do the calculation in the interior only (no overlap) ;
4999 for now, only implemented for SOM advection (to save CPU time).
5000 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
5001 o exch2 adjoint
5002 First set of changes:
5003 - add exch2 hand-written adjoint templates
5004 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
5005 This will require cleanup in pkg/autodiff/*.F
5006 (changed routines currently kept separate in verif. code/)
5007 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
5008 that used to hide exch2 or cubed-sphere specific code
5009 (commented via 'cph-exch2')
5010 o pkg/seaice
5011 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
5012 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
5013 output of global_ocean.cs32x15.thsice .
5014
5015 checkpoint59e (2007/07/26)
5016 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
5017 for B-grid vector (not yet tested) and C-grid vector (<- only used
5018 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
5019 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
5020 (#ifdef ALLOW_SALT_PLUME)
5021 o gather_2d/scatter_2d: removed halo regions
5022 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
5023 scheme and the corresponding test case (under front_relax dir). For now,
5024 only available with Skew-flux form and not yet tested in realistic set-up.
5025 adjoint: store directives updated, but gradient checks deteriorated,
5026 so maybe GM/Redi adjoint is now broken.
5027 o seaice adjoint
5028 * add AREA, HEFF, HSNOW as control variable
5029 (should not change lab_sea results)
5030 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
5031 o pkg/seaice:
5032 * added computation of saltFlux in seaice_growth;
5033 For time being, sea ice salinity is assumed constant
5034 contribution of snow flooding to freshening of sea ice is neglected.
5035 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
5036 defaults to 0.0 in order to maintain backward compatibility.
5037 Typical values for SEAICE_salinity are 4 to 10 g/kg.
5038 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
5039 * added SEAICE_availHeatFrac, which specifies fraction of surface level
5040 heat content used to melt or grow ice
5041 * commented out cap of HICE: it helps keep ice thinner
5042 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
5043 * applied OBCS T/S mask to HEFFM sea ice mask
5044
5045 checkpoint59d (2007/06/21)
5046 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
5047 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
5048 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
5049 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
5050 and change default value of parameter "GM_Small_Number";
5051 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
5052 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
5053 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
5054 o pkg/ecco: cost function when applying pkg/smooth to controls
5055 o pkg/ctrl: add forcingPrecond run time parameter
5056 o pkg/seaice:
5057 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
5058 - fix bug in metric terms of u-equation in LSR solver (implicit part),
5059 changes verification/lab_sea
5060 - rearrange implicit part of u-equation in LSR solver to make it easier to
5061 read, understand, and debug. This causes changes at the truncation level.
5062 - fix (serious) bug in the boundary conditions (sign error in the implicit
5063 part) of the LSR solver. Changes all LSR results.
5064 - fixed problem with HSNOW initialization to avoid thick snow when AREA
5065 is initilized with small values - does not change lab_sea results.
5066 - added HsnowFile initialization capability
5067 o pkg/smooth: addition to model/src and pkg/ctrl so allow
5068 initialization of pkg/smooth and application to control vector
5069 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
5070 o dependencies: pkg/profiles requires pkg/cal
5071 o pkg/profiles:
5072 - added option ALLOW_PROFILES_GENERICGRID
5073 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
5074 that interpolation information (grid points and coefficients) is provided
5075 within the netcdf input files.
5076 -> sample matlab scripts can be found in MITgcm_contrib/gael
5077 that allow you to prepare netcdf input files.
5078 - also modified: cleaner include statements, cleaner error print statements,
5079 cleaner stops when error, and more tests of the netcdf input files consistency.
5080 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
5081 o pkg/seaice:
5082 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
5083 requires a new routine: seaice_diagnostics_fill.F
5084 - make sure that seaice does not move if not forced (pressure replacement
5085 method, Hibler and Ip, 1995), changes results
5086 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
5087 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
5088 It is turned off by default (=-1.), because it changes the results.
5089 - make it possible to read AREA from a file, too.
5090
5091 checkpoint59c (2007/06/04)
5092 o add S/R and diagnostics for oceanic mixed-layer depth
5093 o move GMRedi call after all vertical mixing schemes (including KPP)
5094 o pkg/thsice:
5095 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
5096 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
5097 o pkg/obcs:
5098 - bug fix for balance code
5099 o pkg/seaice:
5100 - allow values of SEAICE_elasticParm > 1
5101 - add new parameter SEAICE_evpTauRelax as an alternative
5102 to SEAICE_elasticParm
5103 - make lsr boundary conditions free slip (by default), changes result
5104 - add code for no slip boundary conditions for lsr
5105 - set minimum of zeta to zero (and not 4e8) (changes results)
5106 - add a cap on AREA after advecting AREA if seaice_growth is not called
5107 o change calculation of Visbeck K:
5108 - no longer depend on tapering scheme; instead, compute slope (limited
5109 by GM_maxSlope). this is equivalent to what was comuted before with
5110 clipping or linear tappering.
5111 - fix vertical averaging (wrong by 1/2 level)
5112 - leave the old version (but will not be maintained) within
5113 #ifdef OLD_VISBECK_CALC / #endif
5114 - update output of exp. ideal_2D_oce
5115 o change error catch in calc_r_star to improve vectorization
5116 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
5117 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
5118 o adjoint:
5119 Re-organized adjoint checkpointing according to Matt Mazloff
5120 (but with modifs/completions/cleanups)
5121 Storing is now bundled into large arrays to optimized I/O
5122 (and second step in cleanup of the_main_loop)
5123
5124 checkpoint59b (2007/05/16)
5125 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
5126 - export/import (between ocean & coupler) fields needed for ocean DIC.
5127 o pkg/seaice:
5128 - get rid of three more exchanges seaice_calc_viscosities (required
5129 different loop boundaries in seaice_lsr and seaice_ocean_stress)
5130 - bug fix in seaice_ocean_stress (update of lab_sea required)
5131 - reduce loop boundaries to necessary minimum also in seaice_evp
5132 - go back to the old way of computing deltaC/Z as the adjoint likes that
5133 better
5134 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
5135 passive tracer to an Age Tracer) + update output.txt
5136 o pkg/exf:
5137 - implement A-grid / C-grid selection for wind-stress input files.
5138 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
5139 for now, in exf_bulk_largeyeager04.F only :
5140 - change implementation for case where windspeed + 2. components wind-stress
5141 are read-in. AND use rhoConstFresh to convert evap.
5142 o pkg/seaice:
5143 - use correct EXCH_UV for wind-forcing (on A-grid).
5144 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
5145 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
5146 o pkg/exf:
5147 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
5148 EXF_INTERPOLATION:
5149 - merge global_with_exf/code version of exf_interp_read.F
5150 to the main code ;
5151 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
5152 reading the file ; Important: This options needs to be defined to recover
5153 previous code.
5154 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
5155 - no longer loose real*8 precision along the way when using exf_iprec=64.
5156 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
5157 - change discretisation of evp-solver in order to avoid another exchange
5158 (changes lab_sea) and clean up a little
5159 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
5160 help the adjoint (this also changes the results slightly)
5161 - add a few "_d 0" where they had been missing in seaice_evp.F
5162 - cleaning up: remove unused seaice_calc_rhs.F
5163 o pkg/exf: some cleaning-up:
5164 - change various "constants" into runtime parameters
5165 - cleaned-up Large&Yeager04 routine which should eventually
5166 replace exf_bulkformulae.F (changed names of S/R and CPP)
5167 and merged various ALLOW_ATM_WIND options
5168 only used with thsice pkg (in thsice_get_exf.F):
5169 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
5170 which are used when useStabilityFct_overIce=TRUE (= the default)
5171 - change default values of ice & snow emissivity and scale downward LW
5172 by ice & snow emissivity.
5173 o pkg/thsice:
5174 fix few little problems, in thsice_calc_thickn.F:
5175 - growth vertically (and not laterally) if iceFrac == iceMaskMax
5176 - melt only laterally if hIce < hThinIce (as the comments say)
5177 and in thsice_extend.F:
5178 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
5179 - start to form ice as soon as the minimum ice-volume is reachable.
5180 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
5181 and cpl_aim+ocn
5182 o pkg/kpp
5183 - move computation of surface related input fields to KPP into a new
5184 subroutine kpp_forcing_surf.F
5185 - remove wrong (within bi,bj loops) EXCH calls.
5186 - little cleaning (add argument myThid in last position, cvs header ...)
5187 - for now, fix conservation problem by exchanging KPPviscAz (may not
5188 be the best fix)
5189 o pkg/seaice
5190 - check for inconsistent evp parameter/cpp-flag combination
5191 - remove leftover errIO flat for obsolete name list error handling
5192 o OpenAD
5193 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
5194
5195 checkpoint59a (2007/05/01)
5196 o pkg/seaice: some parameter clarifications and a little bit of clean up
5197 o pkg/thsice: rename run-time parameters:
5198 himin -> hIceMin
5199 himin0 -> hThinIce
5200 hihig -> hThickIce
5201 i0 -> i0swFrac
5202 transCoef -> bMeltCoef
5203 frac_energy -> fracMelting
5204 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
5205 with default values (for now) that do not change the results.
5206 remove old version of thsice vars advection in pkg/seaice.
5207 o in FFIELDS.h:
5208 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
5209 - make pLoad & sIceLoad always available (but still only used if
5210 ATMOSPHERIC_LOADING is #define).
5211 o pkg/kpp: replaced _KPP_RL with _RL
5212 o bug fixes for vertical diffusivity computations when both KPP and
5213 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
5214 are no longer updating the vertical diffusivity array
5215 (passed as argument) but are (re-) setting those arrays.
5216 o pkg/seaice: fix bug in evp solver, while doing that
5217 - change (improve?) discretization of stress computations for both
5218 cgrid-lsr and evp solver
5219 - add a new routine to compute strain rates
5220 - the above changes lab_sea results
5221 - add no slip conditions for evp solver (off by default), lsr-version
5222 may follow
5223 - fix exchange for shear at Z-points (does not change lab_sea)
5224 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
5225 (to force the user to pick a time step since there is not "safe" way
5226 of choosing it)
5227 - add principal stress diagnostics
5228 - rearrange fields for evp a little to avoid having to call a: too many
5229 exchanges and b: exchanges for stress trensor components which we do
5230 not have.
5231 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
5232 of evp, complete rewrite for lsr case (latter is does not yet work
5233 in all cases)
5234 o pkg/kpp: add code to have mixing in shelf ice caverns
5235 - add myThid to all kpp routines (long overdue)
5236
5237 checkpoint59 (2007/04/19)
5238 o pkg/exf:
5239 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
5240 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
5241 - move exf header files from lower_case.h to UPPER_CASE.h ;
5242 add missing cvs Header & Name
5243 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
5244 - add namelist param. selectStressGridPosition, exf_monFreq
5245 - retire many _CLIM routines, and remove data.exf_clim
5246 + params moved to data.exf
5247 + climsst, climsss now handled by exf_set_gen, i.e.
5248 climss?period=0 refers to constant field,
5249 climss?period=-12 to monthly forcing
5250 - split up namelists in data.exf
5251 o pkg/seaice:
5252 - remove seaice_exch and seaice_exch_uv
5253 - remove superfluous exchange of theta
5254 - add myThid to seaice_budget_ocean/ice
5255 - add new interface for atmospheric wind forcing (C-grid only)
5256 + new routine
5257 + two new field (taux, tauy for stress over ice)
5258 + removed one global field (DAIRN) for C-grid case only
5259 o pkg/thsise
5260 - 2nd set of modifs for thsice adjoint in conjunction with exf
5261 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
5262
5263 checkpoint58y_post (2007/04/15)
5264 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
5265 vertical diffusivity, similar to that in MOM4; turned on using
5266 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
5267 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
5268 o Added capability for 3D specification of background vertical diffusion
5269 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
5270 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
5271 "data" file that contains the 3D vertical diffusivity coefficients.
5272 o ice dynamics (pkg/seaice) with thsice thermodynamics:
5273 - add code within pkg thsice to advect & diffuse sea-ice fields
5274 similar to (and will replace) what has been added in seaice_advdiff.F,
5275 but: - conserving Mass, Heat & Salt.
5276 - better when using non-linear advection scheme (not yet fully tested)
5277 - can also be used in atmospheric set-up (for now, only the diffusion).
5278
5279 checkpoint58x_post (2007/04/04)
5280 o IO option for global-file compact format:
5281 - add options when generating topology (utils/exch2/matlab-topology-generator)
5282 - add I/O capability (pkg/mdsio).
5283 - adapt utils/matlab/rdmds.m to read this format.
5284 for now long-line format not yet supported by pkg/mdsio (& exch2).
5285 o shelfice: add a few diagnostics
5286
5287 checkpoint58w_post (2007/03/13)
5288 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
5289 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
5290 (and replace horiVertRatio in NH code).
5291 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
5292 and tutorial_plume_on_slope (sensitive to truncation)
5293 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
5294 directly to drive seaice model (C-grid only)
5295 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
5296 - reintroduce computation of wind from stress,
5297 - compute tau (in exf_bulkformulae.F) from windstress averaged to
5298 mass points to avoid tau = 0
5299 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
5300 o rdmnc.m: make it work with "global" files created with gluemnc
5301 o rdmnc.m : some improvements in dealing with singleton dimension
5302 (tested on all testreport mnc output files).
5303 o genmake2: disable pkg/profiles if netcdf test fails.
5304 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
5305 o move call to cal_readparms up to make calendar parameters/variable available
5306 to all packages
5307
5308 checkpoint58v_post (2007/02/08)
5309 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
5310 useDynP_inEos_Zc tested.
5311 o pkg/exf: changes to properly interpolate/mask/scale initial fields
5312 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
5313 and portions thereof. See read_cs.txt for description and examples.
5314 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
5315 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
5316 following the great-circle arc between those 2 points.
5317 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
5318 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
5319 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
5320 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
5321 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
5322 - still needs work (not working with some options ; efficiency to improve)
5323 and serious testing.
5324 - use this scheme for temperature & salinity in 2 advection test exp.:
5325 advect_xy & advect_xz, respectively.
5326
5327 checkpoint58u_post (2007/01/12)
5328 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
5329 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
5330 o testreport: add option "-skipdir" to skip some test.
5331 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
5332 momentum calculation.
5333 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
5334 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
5335 remove checkpoint.F and the_correction_step.F (no longer used);
5336 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
5337 o add option (linFSConserveTr) to correct for tracer source/sink due to
5338 Linear Free surface
5339 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
5340 o pkg/thsice: fix reading mnc-pickups
5341
5342 checkpoint58t_post (2006/12/30)
5343 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
5344 o pkg/mdsio:
5345 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
5346 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
5347 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
5348 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
5349 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
5350 either MDS_READ_FIELD or MDS_WRITE_FIELD )
5351 - new S/R (to replace MDSWRITEMETA), which allows to write more
5352 informations (variable names, time ...) to meta files.
5353 - modify rdmds.m to give back the meta file content.
5354 o pkg/diagnostics: change vertical interpolation to be safer, and more
5355 flexible (define p-levels to interpolate to in data.diagnostics);
5356 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
5357 diagnostic pointer.
5358 o pkg/seaice: more cleaning up of seaice_growth, added many comments
5359 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
5360 o fix multi-category seaice:
5361 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
5362 SEAICE_MULTICATEGORY
5363 - fix short wave heat flux
5364 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
5365 and allow to use EVP solver. Change forward lab_sea: test both EVP
5366 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
5367 o Initial check-in of lab_sea adjoint
5368 (very similar to natl_box_adjoint/code_seaice)
5369 * used C-grid and EVP solver
5370 * used KPP, GM/Redi
5371 * uses inAdExact=.TRUE.
5372 * gradient checks fail for both ADM and TLM
5373 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
5374 f.d. gradients actually seem more problematic than ADM, TLM gradients;
5375 issue is related to forward mismatch between g77 an ifort
5376 o pkg/seaice: overhaul of thermodynamics
5377 - growth.F and groatb.F are replaced by new routine seaice_growth.F
5378 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
5379 - move a few global fields out of SEAICE.h into seaice_growth.F and
5380 make them 2D (FICE/QNETO/ ...)
5381 - remove FO (it is the same as QNETO)
5382 - introduce a few local fields to avoid modifying external fields such
5383 as atemp, etc.
5384
5385 checkpoint58s_post (2006/12/11)
5386 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
5387 changed exf_set_gen.F so that
5388 genperiod=0 means input file is one time-constant field and
5389 genperiod=-12 means input file contains 12 monthly means
5390 o CG2D: use pre-computed solver main-diagonal (stored in common block);
5391 this affects truncation error ; generate new output file for exp. which
5392 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
5393 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
5394 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
5395 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
5396 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
5397 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
5398 o start implementation of deep-atmosphere and anelastic formulation
5399 o verification: remove 2nd copy of input files and use script "prepare_run"
5400 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
5401 o mom_common/vecinv/fluxform: fix a few initialisation isssues
5402 o profiles: fix for multithreaded case
5403
5404 o diagnostics: rename few diags:
5405 s/'PRESSURE'/'RCENTER '/g
5406 s/'TICE '/'oceFreez'/g
5407 s/'TAUX '/'oceTAUX '/g
5408 s/'TAUY '/'oceTAUY '/g
5409 s/'SWFLUX '/'oceQsw '/g
5410 s/DIFx/DFxE/g
5411 s/DIFy/DFyE/g
5412 and add few ocean-forcing diagnostics:
5413 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
5414 o modifications to pkg/seaice/growth.F and budget.F, which change results of
5415 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
5416 as actual snow thickness. It now refers everywhere to effective snow
5417 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
5418
5419 checkpoint58r_post (2006/11/17)
5420 o modifications to pkg/seaice/growth.F, which change results of
5421 lab_sea experiment: fixes pertain to melting snow over open water, to
5422 masking EVAP under sea ice, and to using the correct AREA variable for
5423 computations of EVAP, PRECIP, HSNOW, and GHEFF
5424 o add ability to read bathy, salt, and theta using MNC (off by def)
5425 o add flooding algorithm and advection of HSNOW for pkg/seaice;
5426 both are turned off by default and do no change any results
5427 o seaice advection with pkg/thsice: a step toward the use of non-linear
5428 advection scheme, but #ifdef or commented out for now (requires more EXCH).
5429 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
5430 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
5431 in natl_box (affects results @ truncation level: update output.txt)
5432 o multi-threading and IO:
5433 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
5434 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
5435 (needed to work with SingleCpuIO): tested in all verif. exp.
5436 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
5437 affects the results (but none of the verification test uses this scheme).
5438 o Adding some pkg/diagnostics capability to pkg/seaice
5439 (will certainly be subject to changes)
5440 o ctrl: adding new control variables:
5441 lwflux, lwdown, evap, snowprecip, apressure, runoff
5442
5443 checkpoint58q_post (2006/10/20)
5444 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
5445 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
5446 high_res_cube configuration by 4% on Columbia.
5447 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
5448 add (in global_with_exf/code) a version of EXF_INTERP_READ without
5449 dynamical allocation (seems to work in multi-threaded).
5450 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
5451 single CPU io) so that TAF does not have to see EESUPPORT.h
5452 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
5453
5454 checkpoint58p_post (2006/09/08)
5455 o obcs: stop if obcs is used with useCDscheme = .true.
5456 o shelfice:
5457 - fix a sign error so that no slip at shelfice interface works
5458 - remove stop for combination non-hydrostatic code and shelfice. That does
5459 not mean, that the results are correct, but at least they are numerically
5460 stable
5461 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
5462 o added adjoint exch routined for all exch*3d* routines
5463 and updated flow directives
5464
5465 checkpoint58o_post (2006/08/28)
5466 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
5467 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
5468 o change controling S/R for writing pickup file (new S/R do_write_pickup)
5469 and clean-up reading/writing of pickup files.
5470 o fix local version of read/write pickup (NH part) in rotating_tank/code
5471 o simplify EXCH interface:
5472 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
5473 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
5474 o added the regrid package
5475 o shelfice:
5476 - add a simple boundary layer scheme to reduce noise
5477 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
5478
5479 checkpoint58n_post (2006/08/14)
5480 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
5481 local variable (not in common block).
5482 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
5483 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
5484 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
5485 to work with SingleCpuIO.
5486 o add "_d 0" to real constant of pkg/cfc subroutines ;
5487 update exp. cfc_exemple & tutorial_cfc_offline output files.
5488 o multi-threading and IO:
5489 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
5490 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
5491 - barrier before and after reading.
5492 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
5493 - avoid using MDS_WRITELOCAL for LAND pkg output.
5494 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
5495 common-block variables ; Allows multi-threading with master-thread IO.
5496 o change default MAX_NO_THREADS from 32 to 4 ;
5497 and stop cleanly when MAX_NO_THREADS is too small.
5498 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
5499
5500 checkpoint58m_post (2006/07/17)
5501 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
5502 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
5503 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
5504 keep global_ocean.90x40x15 (for AD testing) with former secondary test
5505 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
5506 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
5507 add MITgcm_tutorials (= code + all the tutorials)
5508 o ecco, option to compute cost for total ssh (mean+anom)
5509 o consistent with addition of ptracer and ssh in pkg/profiles
5510 o profiles: adding ptracer and ssh
5511 o testreport: change multi-test output-file name
5512 (from output.txt.{name} to output.{name}.txt)
5513 o profiles: now ok for mutli-tiles case
5514 o seaice: add 4 parameters for different advection schemes for area,
5515 (effective) seaice thickness, enthalphy, and snow height. Their default
5516 is the standard parameter SEAICEadvScheme
5517 o calc_gw:
5518 - add cosFacU in zonal viscous flux (harmonic.visc.).
5519 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
5520 of tutorial_plume_on_slope.
5521 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
5522 o calc_gw: true flux-form, account for horizontal grid spacing.
5523 update rotating_tank results, but not plume_on_slope (affected at
5524 truncation level, 11 digits).
5525
5526 checkpoint58l_post (2006/07/12)
5527 o calc_gw:
5528 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
5529 - remove side-drag for now (need to fix it); update plume_on_slope results.
5530 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
5531 o commit code to make SST/SSS weights spatially variable
5532 (based on either variable in-situ or variable initial T/S weights)
5533 o pkg/ecco:
5534 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
5535 now based on horizontally varying weights wthetaLev, wsaltLev
5536 * cost_averagesflags now returns year indices in addition to day, month
5537 * sflux balance is performed on annual basis
5538 (sflxumm, sfluxmm2, bal_sfluxmm)
5539 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
5540 including separate counting and multipliers
5541 o pkg/rbcs
5542 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
5543
5544 checkpoint58k_post (2006/07/06)
5545 o testreport:
5546 - always build in dir. "build" (if not there, mkdir build instead of building
5547 & running in input)
5548 - run in dir run (if it exists), in build otherwise.
5549 - call prepare_run (if input/prepare_run exists)
5550 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
5551 o pkg/exf modifications to interpolation and rotation routines for more
5552 reasonable treatment of North Pole singularity: for tracers North Pole
5553 value is set to northernmost zonal-mean value, for zonal velocity it is
5554 set to zero, and for meridional velocity it is set to northernmost value.
5555 o pkg/exf/exf_check_range.F
5556 - add tile index to diagnostics and move stop statement to the very
5557 end of the routine.
5558 o pkg/diagnostics: (diagnostics_main_init.F)
5559 define title of isomorphic variables according to the current config.
5560 o pkg/thsice with pkg/seaice dynamics:
5561 - fix domain of computation (interior only, required for exf) and do exchanges
5562 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
5563 o towards a standard way of dealing with multi-threading in MONITOR
5564 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
5565 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
5566 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
5567 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
5568 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
5569 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
5570 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
5571 o tracer advection:
5572 - clean-up and simplify calc_common_factors.F
5573 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
5574 advection subroutine (but still not used within DST advection S/R)
5575 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
5576
5577 checkpoint58j_post (2006/06/15)
5578 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
5579 from file (collects calls previously in FORWARD_STEP)
5580 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
5581 o adjoint store dir. adjusted accordingly
5582 o genmake2
5583 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
5584
5585 checkpoint58i_post (2006/06/14)
5586 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
5587 on wind stress (SEAICEstressFactor defaults to 1.)
5588 o Total number of Timers is finite (<=40): comment out 2 non-essential one
5589 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
5590 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
5591 on CS-grid: no longer loosing mass.
5592 o exf & curvilinear-grid: no longer modify longitude xC & xG.
5593 o pkg/ggl90: fix sloppy output and fix a bug
5594 o pkg/seaice: added SEAICEuseEVPpickup parameter
5595 - Set to false in order to start EVP solver with
5596 non-EVP pickup files when using SEAICEuseEVP
5597 - fix sign error in diffusion in seaice_calc_rhs
5598
5599 checkpoint58h_post (2006/06/07)
5600 * Modifications for bottom topography control
5601 o replace hFacC by _hFacC at various places
5602 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
5603 o add non-self-adjoint cg2d_nsa
5604 o update autodiff support routines
5605 o re-initialise hfac after ctrl_depth_ini
5606 o works for 5x5 box, doesnt work for global_ocean.90x40x15
5607 * Adding verification for 5x5 box (4-layer) bottom topography control
5608
5609 checkpoint58g_post (2006/06/07)
5610 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
5611 used for mean seasonal cycle, mean diurnal cycle); add an example
5612 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
5613 o pkg/ggl90:
5614 - add parameter (minimum surface kinetic energy)
5615 - fix bug (avoiding division by zero)
5616 o couple pkg/thsice to pkg/seaice:
5617 - modify advection in seaice to accomodate new scalar fields to be advected
5618 - only muliDimAdection scheme work with seaice/thsice
5619 - mapping of thsice-variables to seaice-variables, back and forth
5620 - does not break the verification experiments, but does not give the
5621 desired results either
5622 o pkg/seaice
5623 - make (default) second order advection a bit less confusing?
5624
5625 checkpoint58f_post (2006/06/05)
5626 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
5627 to pkg/seaice):
5628 - new routines thsice_map_exf and thsice_get_exf provide the interface
5629 - add an additional formal parameter to thsice_solve4temp
5630 o pkg/exf:
5631 - add new fields wspeed, snowprecip (to be able to couple to thsice)
5632 - correct Stefan-Boltzmann constant
5633 - new parameter for longwave surface emittance
5634 - separate some stuff from exf_bulkformulae into new routines
5635 exf_radiation, exf_wind
5636 - add new parameters and constants: longwave emissivity for ocean, ice
5637 and snow, evaporation parameters over ice
5638 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
5639 either wind from stress or stress from wind
5640 o pkg/thSIce:
5641 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
5642 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
5643 and THSICE_CALC_THICKN
5644 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
5645 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
5646 to make debugging easier.
5647 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
5648 o pkg/bulk_force:
5649 - clean-up comments and parameters ;
5650 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
5651 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
5652 generate new output for test-experiment: aim.5l_cs.thSI
5653 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
5654 testreport accordingly
5655
5656 checkpoint58e_post (2006/05/17)
5657 o SEAICE_CGRID adjoint done
5658 o R_STAR adjoint implemented.
5659 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
5660 * need to sort out init. of h0facc, etc.
5661 o Make pkg/profile fully independent of ecco,cost, etc. stuff
5662 to be able to use it in pure forward.
5663
5664 checkpoint58d_post (2006/04/21)
5665 o upgrade simple test-experiment to tutorial example:
5666 step.1: duplicate the experiment and (step.2) will remove the old copy.
5667 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
5668 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
5669 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
5670 tutorial_global_oce_biogeo <- copy of dic_example
5671 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
5672 tutorial_plume_on_slope <- copy of plume_on_slope
5673 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
5674 tutorial_global_oce_optim <- empty for now (David ?)
5675 tutorial_global_oce_in_p <- copy of global_ocean_pressure
5676 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
5677 o correct a sign problem in cost_scat.F
5678 o obcs and ptracers: fix boundary conditions for advections schemes
5679 with larger stencil
5680 o thsice adjoint: start
5681 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
5682 completeness
5683 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
5684 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
5685 o ptracers adjoint:
5686 * avoid extensive recomputatations
5687 * fix missing re-init. of gptr (missed by TAF)
5688 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
5689 me to turn off the excessive output to STDOUT that this package produces
5690 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
5691 and add those terms in Vector-Invariant formulation.
5692 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
5693 if the control period (xx_hfluxperiod etc) is 0
5694 o in profiles pkg, clean routines and fix details
5695 o in ecco pkg, reading ssh data:
5696 fix problem in case the model does not start at iter0=0
5697 o fix mnc-pickup/restart for ptracers
5698 o new package prifiles:
5699 code to compute profile-based cost by Gael Forget
5700 (modifs in ecco, ctrl, autodiff)
5701 o Benign bug fix in initialization (spotted by M. Mazloff) of
5702 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
5703
5704 checkpoint58c_post (2006/03/23)
5705 o adjoint: finish NLFS adjoint and provide reference output in
5706 verification/global_ocean.90x40x15/results_ad_nlfs
5707 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
5708 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
5709 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
5710 with SEAICE_CGRID defined.
5711 o move calendarDumps from "data" to "data.cal" and clean-up the code
5712 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
5713 o add useEXF & useCAL flags (for now, set in hard-coded way)
5714 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
5715 (were missing in NH mode, and wrong in quasihydrostatic mode).
5716 waiting for Chris updated version of calc_gw to add those CALLs.
5717 o fix bug in quasihydrostatic S/R ;
5718 add a test for this option: global_ocean.90x40x15.qshyd
5719 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
5720 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
5721 o add on/off flag useOffLine for package OFFLINE
5722 o seaice:
5723 - modify advection so that it works also on the C-grid
5724 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
5725 problem in multi-tile runs with C-grid
5726 - add flags for clipping ice velocities and/or masking solver forcing
5727 - fix drag (ocean on ice) formulation and a bug that caused noise in the
5728 C-grid solver
5729 - added a few comments to seaice_diffusion.F
5730 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
5731 are now exclusive)
5732 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
5733 required re-ordering the code a little:
5734 + make DAIRN global variable (defined in SEAICE)
5735 + move computation of the viscosities eta and zeta into a new separate
5736 routine (because I need to recompute them in seaice_ocean_stress.F)
5737
5738 checkpoint58b_post (2006/03/13)
5739 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
5740 update output.txt of exp. aim.5l_cs.thSI
5741 o various mnc cleanups and improvements:
5742 + shrink lookup tables by factor of ~4
5743 + better error reporting when running out of lookup space
5744 + able to handle longer path/file names (up to 500 chars)
5745 o adjoint:
5746 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
5747 - TBD: "hidden" mom_vecinv recomp. in dynamics
5748 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
5749 (allow to differentiate between forcing components using new integer flags:
5750 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
5751 and add new flag to put Dissipation tendency out of Adams-Bashforth.
5752 o ecco
5753 - enable trend removal from SSH anomaly obs.
5754 o adjoint
5755 - a fix for PmEpR when #undef EXACT_CONSERV
5756 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
5757 - try to fix "hidden" recomp. in forward_step for NLFS
5758 (NLFS seems broken sometimes after I checked it in)
5759 o seaice:
5760 - add c-grid version of the dynamic solver:
5761 + three new routines that are the c-grid substitute lsr, dynsolver
5762 and ostres
5763 + put a few fields that were local to dynsolver into global common
5764 blocks, so that I can move the computation of stresses etc into
5765 seaice_lsr (saves coding but may break the adjoint).
5766 - replace more hardwired parameters by runtime parameters
5767 - add ice masks that mask the rhs of the implicit solvers where there
5768 is no ice (commented out in seaice_dynsolver, because i am not sure
5769 if this works properly), eventually this should replace the clipping
5770 of ice velocities in seaice_dynsolver to +/-40cm/s.
5771 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
5772 include it only where its needed
5773 o move balancing of fluxes before the call of external_forcing_surf
5774 o seaice:
5775 - correct units of turning angles (now they are really in degrees)
5776 - move computation of GWATX/Y out of main routine into dynsolver
5777 - initialize GWATX/Y in seaice_init
5778 o Apply mask on Fresh-Water flux (needed for SSH forcing).
5779 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
5780 o seaice: add runtime flags for turning angles (default to zero)
5781 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
5782 and trend from exf forcing and ctrl control adjustments
5783 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
5784 (since checkpoint57x_post)
5785 o change the default rotation period to 86164.s = the Earth rotation
5786 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
5787 and based on a reference stratification. Tested within hs94.cs-32x32x5.
5788 o seaice advection: add code for choosing between the default (2nd order
5789 central differences) and multiDim advection schemes provided by
5790 pkg/generic_advdiff
5791 o seaice:
5792 - removed all references to SEAICE_GRID.h fields from
5793 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
5794 (cubed-sphere configuration will change a little)
5795 - grid computations in seaice_init are obsolete now.
5796 - cleaned up code a little so that is easier to read (hopefully).
5797 - added new (better?) discretizations of default advection and diffusion
5798 (turn on with SEAICEuseFluxForm)
5799 - replace 1 in 3d global fields by kSurface in growth.F
5800
5801 checkpoint58a_post (2006/02/13)
5802 o seaice:
5803 - bug fix in advect.F
5804 o shelfice:
5805 - separate shelfice load anomaly from pload (breaks with time
5806 dependent forcing), => introduce constant field shelficeLoadAnomaly.
5807 Its default is 0., but it may be computed more cleverly from (unknown)
5808 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
5809 done offline. A good approximation of the pressure load anomaly is
5810 necessary to avoid large initial adjustment processes underneath
5811 deep-reaching shelfice.
5812 - small fix in ISOMIP shelfice_thermodynamics
5813 - add more sophisticated thermodynamics of Hellmer (1989), this is
5814 now the default
5815 - give a few constants more intuitive names
5816 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
5817 if bulk formulae are used in long integration (especially EmPmR). Turn
5818 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
5819 if balancePrintMean, the imbalance that is substracted is printed to
5820 STDOUT.
5821 o fix bug (typo) in obcs_apply_eta.F
5822 o add a new package shelfice which enables us to model the circulation
5823 underneath shelf-ice with draughts of hundreds of meters.
5824 - works
5825 - to do: + include improved thermodynamics
5826 + check whether kSurfC (from model/inc/SURFACE.h) can be used
5827 instead of new field kTopC
5828 + can we use topoFile, Ro_surf and existing code in ini_depth.F
5829 instead of new field R_shelfIce and new code in ini_depth.F
5830 and ini_mask_etc.F?
5831 + adjust vertical mixing schemes?
5832 o seaice pkg:
5833 - add a cpp-flag to include a simple formula for a salinity dependent
5834 freezing point of sea water at the surface
5835 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
5836 meridional stresses are now different (and hopefully correct)
5837 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
5838 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
5839 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
5840 o pkg/diagnostics: add options and parameters for regional-statistics
5841 diagnostics ; define regions by reading a region-mask from a file
5842 (might add other options later)
5843 o pkg/bulk_force:
5844 - add option and parameters to use AIM surface-flux formulae.
5845 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
5846 others forcing fields (defined in PARM05, parameter file "data") are loaded
5847 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
5848 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
5849 - use the right EXCH call for uwind,vwind (to work on CS-grid).
5850 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
5851 and parameters (note: calcWindStress replaces .NOT.readwindstress).
5852 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
5853
5854 checkpoint58 (2006/01/12)
5855 o add "--embed-source" option to genmake2 which, when the supporting
5856 tools can be compiled (as determined by genmake2) will turn on the
5857 embed_files package which then embeds the entire MITgcm source code
5858 (*.[fFhc] + Makefile) used for the build within the executable
5859 - requested by CNH but off by default
5860 - adds a paltry <9MB to the mitgcmuv executable in most cases
5861 - only writes the output when useEMBEDSRC in eedata is true
5862 o clean up 3-dim. relaxation codes:
5863 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
5864 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
5865 * Thanks to Tom Haine for testing!
5866
5867 checkpoint57z_post (2005/12/31)
5868 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
5869 affects output (@ truncation level) of exp. plume_on_slope ; updated.
5870 o fix the pickup behavior for obcs in combination with ptracers
5871 o fix a bug in ptracers_external_fields_load
5872 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
5873 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
5874 o transfered surface NH pressure to eta field (if exactConserv).
5875 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
5876 and update lab_sea output.txt file.
5877 o completing 3-dim. relaxation code: additional term
5878 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
5879 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
5880 * At compile time, in "EXF_OPTIONS.h" set
5881 #define ALLOW_CLIMTEMP_RELAXATION
5882 #define ALLOW_CLIMSALT_RELAXATION
5883 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
5884 tauThetaClimRelax3Dim = 15552000.0,
5885 tauSaltClimRelax3Dim = 15552000.0,
5886 * 3 cases:
5887 1) Use a constant-in-time 3-dim. field
5888 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
5889 3) Real-time relax. to time-evolving prescribed field
5890 o Adding Laplacian-type smoothness constraint on
5891 initial and boundary (forcing) controls (ic, bc)
5892 * enable at compile-time via
5893 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
5894 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
5895 * Absolute scale somewhat unclear so far
5896 * no area weighting was included since no other cost term does so far
5897
5898 checkpoint57y_post (2005/12/08)
5899 First step for a NLFS adjoint
5900 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
5901 o new init. routines for calc_r_star, calc_surf_dr
5902 o still need to deal with ini_masks_etc
5903 o testreport seemed happy
5904 checkpoint57y_pre (2005/12/08)
5905
5906 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
5907 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
5908 o add new offset feature to offline pkg (plus minor cleanup)
5909 o cfc fixes for final year of integration
5910 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
5911 be in GCHEM_OPTIONS).
5912
5913 checkpoint57x_post (2005/12/04)
5914 o fix testreport Pb in multiple test experiment.
5915 o cleanup our namelist syntax in verification:
5916 - make it more F95 standards compliant (some work still needed)
5917 - allows the vast majority of our tests to work with gfortran
5918 o Non-Hydrostatic:
5919 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
5920 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
5921 o Allow to apply AB on T,S rather than on AB(gT,gS):
5922 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
5923 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
5924 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
5925 - need a "clever" read_pickup to restart from the other AB formulation
5926 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
5927 o remove some unused variables (reduces number of compiler warnings)
5928 o adjoint
5929 * Disable useVariableViscosity for adjoint for time being
5930 (there are a number of extensive recomputations)
5931 * Initialize certain variables needed for adjoint
5932
5933 checkpoint57w_post (2005/11/03)
5934 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
5935 fix the singleCpuIO RS version of MDSWRITEFIELD
5936 and add a WARNING if using globalFiles=T with multi-processors.
5937 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
5938 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
5939 o tracer advection scheme:
5940 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
5941 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
5942 was not very convenient).
5943 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
5944 (further tests needed for the implicit DST & Flux-Limiter schemes).
5945 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
5946 and sRef for convenience, handy, when you want to initialize
5947 ptracers in a large domain with a constant non-zero value. Also,
5948 untangle ptracers_init.F a little.
5949
5950 checkpoint57v_post (2005/10/13)
5951 o change dome exp. to use variable viscosity in side-drag terms.
5952 o remove all the files from the cfc_offline test since they are now
5953 incorporated into tutorial_cfc_offline which has been producing
5954 identical results for a few days of testing
5955 o add new parameter: sideDragFactor to enable half-slip-side BC
5956 and change side-drag S/R to use viscosity from mom_calc_visc
5957 (can switch back by setting sideDragFactor=0.); affects results at
5958 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
5959 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
5960 o vorticity & strain are now computed without masking, to account for
5961 no-slip-side BC in variable viscosity calculation ; mask is applied
5962 anyway later on, before computing advection/coriolis terms.
5963 o modify exp4 to test new obcs support for reading from external files
5964 and for passive tracers
5965 o fix behavior of ptracers_monitor when monitor output is written to a
5966 netcdf-file; still not independent of monitor.F (writes in the same
5967 file).
5968 o change default value of tRef (put a uniform, meaningful value for ocean
5969 & atmos) and initialize sRef (was missing, as Martin mentioned).
5970 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
5971 to be proportional to enstrophy dissipation length. Thus,
5972 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
5973 This is now consistent with Smagorinsky and with the manual.
5974
5975 checkpoint57u_post
5976 o OBCS and PTRACERS: add open boundary support for passive tracers
5977 - either use homogenous (pseudo) v.Neumann conditions or prescribe
5978 OB-values from file; this is not different from the way theta and salinity
5979 are treated
5980 - however, Orlanski-radiation conditions are not supported, and the model
5981 will stop if you use pTracers and Orlanski at the same time.
5982 - beefed up the rountine obcs_external_fields_load: now only those open
5983 boundary values are overwritten with values from files for which there
5984 are really files, otherwise the OB-fields remain untouched. This makes
5985 it possible to use different OBs at different ends of the domain (as
5986 with EXF)
5987 o reduce number of exch calls in shap_filt (s2).
5988 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
5989 truncation level) 4/5 MLAdjust test results (11&12 digits match).
5990
5991 checkpoint57t_post (2005/10/03)
5992 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
5993 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
5994 same truncation, independent of the face number: affects affects several
5995 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
5996 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
5997 note that biharmonic viscosity + no-slip was not tested in any experiment.
5998 o fix bug in non-linear free-surf side-drag ; generate new output for
5999 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
6000 o make mnc honor the writeBinaryPrec flag for most kinds of output
6001 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
6002 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
6003 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
6004 o add brackets in multi-terms sum to get same truncation, independent of
6005 the face number (manage to get exactly same value of gU,gV at the cs-edge)
6006 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
6007 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
6008 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
6009 a maximum grid-scale Reynolds number. Also, changes all length calculations
6010 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
6011 Suggested values of viscosity parameters found in mom_calc_visc.
6012 Many new viscosity diagnostics available.
6013
6014 checkpoint57s_post (2005/09/20)
6015 o Add clearing-house for viscosity calculations, mom_calc_visc and
6016 correct numerous bugs in LeithD and Smagorinsky discretizations.
6017 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
6018 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
6019 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
6020 and with Strain-Tension viscous term calculation (mom_hdissip.F).
6021 The Strain-Tension form is now called with useStrainTensonVisc=.true.
6022 ViscAhStrain and viscAhTension are now retired.
6023 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
6024 o In response to JMC's bug report, genmake2 now ignores any soft-links
6025 that it finds in the *current* directory when searching for files.
6026 Soft-links found in any other source directories will still work as
6027 they did before.
6028 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
6029 a C routine to unlimit the stack size
6030 o mnc-ify pkg/aim snapshot vars
6031 o mnc-ify pkg/land as requested by Daniel
6032 o various changes to mnc including:
6033 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
6034 - output can now be grouped so that all files within a group
6035 change the ITER portion of their names in lock-step together
6036 - can now read ("global") PER-FACE (in addition to PER-TILE) files
6037 and works with both EXCH1 and EXCH2 (but needs more testing)
6038 - writing works for all verification test cases w/ g77 on Linux
6039
6040 checkpoint57r_post (2005/09/07)
6041 o make MNC variable initialization happen earlier
6042 o add diagnostics for (almost) each term of the momentum Eq.
6043 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
6044 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
6045 o remove MINIMAL_TAVE_OUTPUT option ;
6046 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
6047 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
6048 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
6049 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
6050 o add time-dependent SST, SSS control
6051 o cost terms in ecco/ modularized (new cost_generic.F)
6052 o cost_averages routines are modularized (new cost_averagesgeneric.F)
6053 o new infrastructure for seaice model vs. obs misfits in seaice/
6054 * driver from the_main_loop.F is seaice_cost_driver.F
6055 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
6056 * gradient check in Exp. 6a of natl_box_adjoint/
6057 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
6058 (see README file)
6059
6060 checkpoint57q_post (2005/08/19)
6061 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
6062 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
6063 - bug was reported by Jean-Michel and Ian Fenty
6064 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
6065 update exp. cpl_aim+ocn output.
6066 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
6067 Needed for high-res. runs with large global files
6068 to be able to limit tapelev size
6069 o Changed some tests for adjoint:
6070 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
6071 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
6072 * global_ocean.90x40x15/ back to default 3-level checkpointing
6073 o Modifications to enable scripted COMMON to MODULE conversion
6074 * verification/OpenAD/code/ has necessary scripts and description;
6075 * converts, compiles and runs successfully;
6076
6077 checkpoint57p_post (2005/08/01)
6078 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
6079 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
6080 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
6081 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
6082 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
6083 (was already the case for dissipation with mom_vecinv,
6084 and also the case for grad.PhiHyd when staggered-timeStep)
6085 This will allow to put dissipation out-off the AB time-stepping.
6086 Unfortunately, affects truncation error. Update output of exp. that "fails"
6087 (cg2d matching number) and leave the others for later: front_relax(10),
6088 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
6089 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
6090
6091 checkpoint57o_post (2005/07/30)
6092 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
6093 (2) its ready to be documented during the 20050801 DocFest
6094 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
6095 for ideal_2D_oce and lab_sea on linux_ia32_g77
6096 o set to #undef CTRL_SET_OLD_MAXCVARS_30
6097 in global1x1_tot/code_seaice_adj to access indices 32, 33
6098 (worth another tag)
6099
6100 checkpoint57n_post (2005/07/29)
6101 o adding precip control xx_precip 32
6102 o adding swflux control xx_swflux 33
6103 o Replacing 10 forcing penalty cost routines by 1 generic.
6104 o Implementing partitioning in time-mean and variable adjustment
6105 for atmos. state.
6106 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
6107 o in natl_box_adjoint:
6108 * updated exp 1 to 10
6109 (but does not have time-mean vs. variable split results yet)
6110 o updated global1x1/*_seaice_adj/
6111 to incorporate latest changes
6112 o enable useSingleCpuIO for mdsio vector routines
6113 (applies in particular to tapelev I/O)
6114 o removed inefficient K-loop in all active_file*control*.F
6115
6116 checkpoint57m_post (2005/07/28)
6117 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
6118 and advect_cs (use EXCH-2 and standard cs-32 grid files).
6119 o pkg/exch2: filling of face-corner halo regions is optional
6120 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
6121
6122 checkpoint57l_post (2005/07/14)
6123 tag before updating tutorials (pre-release-2)
6124 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
6125 for output and interpolation of input fields onto model grid)
6126 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
6127 Affects results of exp. rotating_tank ; update output.txt.
6128 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
6129 and taking the square quantity and/or using a fraction-weight field.
6130 o fix aim_diagnostics_init.F mate numbers.
6131 o add mnc output capability to diagnostics/diagstat and update
6132 our cvsignore files for the ACSII output generated
6133
6134 checkpoint57k_post (2005/07/02)
6135 o lab_sea now uses diagnostics package and provides a suite of
6136 new EXF diagnostics output.
6137
6138 checkpoint57j_post (2005/06/30)
6139 o exf
6140 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
6141 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
6142 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
6143 * extended diagnostics output
6144 - now includes all EXF variables
6145 - hs, hl moved to common block
6146 - separate S/R for diagnostics, called after ctrl vector is added
6147 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
6148 - EXFqnet contains true Qnet (i.e. includes qsw)
6149 * updated verif. lab_sea, global_with_exf
6150 * Rearranging hflux (exf_mapfields -> exf_getforcing)
6151 to ensure that diagnostics sees a true EXFqnet
6152 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
6153 o diagnostics pkg: change pointers so that 1 diagnostic can be used
6154 several times with different frequencies.
6155 o mnc-ify the thsice package as requested by Daniel Enderton
6156 - the monitor--MNC output needs work
6157 - many attributes need to be added (most are currently blank)
6158 o mnc-ify theaim_v23 package as requested by Daniel Enderton
6159 - many attributes need to be added (most are currently blank)
6160 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
6161 o add Sadourny like discretization to the 4th.O vorticity advection scheme
6162 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
6163 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
6164 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
6165 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
6166 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
6167
6168 checkpoint57i_post (2005/06/19)
6169 o Diagnostics package was changed: diagnostic allocation is now deactivated
6170 by setting an empty file name in the namelist (used to be by setting 0 frequency)
6171 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
6172 add 1rst Order upwind vertical Shear.
6173 o add a quick fix for A/B checkpointing in OFFLINE mode
6174 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
6175 end-run around the C/Fortran linking horror in eesup/src/timers.F
6176 o added pkg/runclock: allows user to terminate run based on wall clock
6177 o added non-hydrostatic scaling parameter: nh_am2
6178 o pkg/my82: futile attempt to make results compiler-independent by adding
6179 some "_d 0", etc. no effect.
6180 o for mnc output, fill the 'T' coordinate var with myTime and create a
6181 separate 'iter' variable for iteration count
6182 o pkg/diagnostics:
6183 add new capability: output of Global/Regional & per-level statistics ;
6184 tested against monitor output (including land & thSIce) on various exp.
6185 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
6186
6187 checkpoint57h_done (2005/05/19)
6188 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
6189 data.diagnostics, data.gchem, data.ptracers) is done.
6190
6191 o pkg/diagnostics: prepare for Global/Regional statistics.
6192 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
6193 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
6194 and rename it: DIFFERENT_MULTIPLE
6195
6196 checkpoint57h_post (2005/05/14)
6197 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
6198 o pkg/diagnostics: change output frequency, now in seconds (instead
6199 of Nb of iterations). This requires to change data.diagnostics.
6200 checkpoint57h_pre (2005/05/12)
6201
6202 o in mnc, let the user create the output dir if both mnc_outdir_date
6203 and mnc_outdir_num are false
6204 o add fflags() to pkg/diagnostics which allows one to specify, on a
6205 per-file basis, the file precision [default behavior is unchanged]
6206 o added diagnostics to pkg/kpp, including computation of mixed layer
6207 depth based on a temperature/density criterion
6208 o updated verification/natl_box to test the new pkg/kpp diagnostics
6209 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
6210 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
6211 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
6212 not mnc -- this mistake was found by JMC and is now corrected
6213
6214 checkpoint57g_post (2005/04/15)
6215 o add Adams-Bashforth 3rd Order time stepping:
6216 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
6217 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
6218 checkpoint57g_pre (2005/04/15)
6219
6220 o make lambda[Theta,Salt]ClimRelax spatially varying
6221 (default remains spatially uniform constant based on tau)
6222 o added new control variables
6223 * init. uVel, vVel, etanN
6224 * lambda[Theta,Salt]ClimRelax
6225 o separate masks used for ctrl_pack/unpack 'from write_grid' output
6226 (suggested by G. Forget)
6227
6228 checkpoint57f_post (2005/04/06)
6229 o add parameter "baseTime" = model base time = time at iteration zero
6230 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
6231 account for baseTime shift
6232 o move Coriolis arrays from PARAMS.h to GRID.h
6233 checkpoint57f_pre (2005/04/06)
6234
6235 o mnc-ifying the seaice package
6236 o introduced an alternative length scale calculation for use in the limiting
6237 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
6238 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
6239 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
6240 as well as grad(vort3). Made it compatible with both approximate form
6241 for the cubed sphere and full form of these gradients. Added flag
6242 useFullLeith to select between approximate and full form.
6243 o add "d0" in getcon.F to reduce differences between compilers/platforms
6244 update output.txt of exp. fizhi-gridalt-hs
6245 o change port_rand funtion to allow to set the seed.
6246 o fix obscure MNC bug involving conversion between reals and integers
6247 - it caused no problems with certain (eg. gcc, ifc) compilers but the
6248 new version is now more standards-compliant
6249 o adjoint-related modifications
6250 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
6251 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
6252 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
6253
6254 checkpoint57e_post (2005/02/28)
6255 o Adding eddy stress controls a la Ferreira et al.
6256 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
6257
6258 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
6259 update output.txt of exp. fizhi-gridalt-hs
6260 o add more "Z" dimensions and associated coordinate vars to MNC
6261 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
6262 o parameter calendarDumps: when set, approximate months (30-31 days) and years
6263 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
6264 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
6265 months and years. Requires pkg/cal.
6266 o diagnostics: add pickup functionality
6267 - off by default for backwards compatibility
6268 - current version only uses MDSIO -- MNC will be added
6269 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
6270 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
6271
6272 checkpoint57d_post (2005/02/11)
6273 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
6274 o modify verification/ideal_2D_oce so that it tests the creation of mnc
6275 output from the diagnostics package
6276 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
6277 o make genmake2 more portable by using ".$FS" instead of ".f" for more
6278 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
6279 o add coordinate variables to the MNC output from the diagnostics package
6280 o change MNC-flags default value: true when useMNC=TRUE
6281 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
6282 the ability (off by default) to read the grid information using MNC
6283 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
6284 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
6285 o do snap-shot diagnostics at the middle of the time-interval (instead of
6286 at the end).
6287 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
6288 new test for AIM with thSIce + slab-ocean
6289 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
6290 o move state variable diagnostics to the beginning of the time step ;
6291 (note: still needs some work specially for snap-shot diagnostics)
6292 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
6293
6294 checkpoint57c_post (2005/01/27)
6295 o Change testing option (-ieee) to get closer agreement between g77 & ifort
6296 o generate new output.txt files on faulks with g77 & the new -ieee option
6297 checkpoint57c_pre (2005/01/27)
6298
6299 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
6300 update output.txt of exp. global_ocean.90x40x15
6301 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
6302 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
6303 o add saltFlux(+File) forcing capability with periodicExternalForcing
6304 o allow to use pkg diagnostics for GM-Redi & ThSIce output
6305 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
6306 o improvements for the MNC output from DIAGNOSTICS:
6307 - correct handling of the unlimitied dimension
6308 - all dims now have associated coordinate variables
6309 - variables located at U, V, and Corner ("Z") points are now written
6310 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
6311 *all* data points are output
6312 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
6313 o added pkg/seaice/seaice_monitor.F
6314 o mdsio_readfield.F can now read files visible only to master MPI process.
6315 o pkg/seaice: some test code for ice-modified ocean stress
6316 o exf_getffields interpolation defaults to bilinear for all scalar forcing
6317 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
6318 spurious negative numbers for precipitation and humidity. Will cause
6319 some small numerical differences for integrations using pkg/exf/exf_interp.F.
6320 o pkg/ctrl/
6321 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
6322 May be enabled via doPackDiag
6323 * introduce z-scaling of
6324 + gradient (doZscalePack) and
6325 + control (doZscaleUnpack)
6326 o pkg/mdsio/
6327 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
6328 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
6329
6330 checkpoint57b_post (2004/12/20)
6331 o simplify options in diagnostics_fill arguments (remove weird combinations)
6332 o fix MNC coordinate variables so that they now contain per-face index
6333 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
6334 general, EXCH2 grids are only aligned to a "local" coordinate system
6335 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
6336 o Implement instantaneous output within pkg diagnostics:
6337 setting a negative frequency in data.diagnostics produces
6338 "snap-shot" output (as opposed to time-average if freq > 0)
6339 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
6340 NOTE: change ptracer diagnostics name: use 2 characters to work with
6341 more than 9 tracers. Add also diagnostics of advect & diffus flux.
6342 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
6343 becomes the coordinate variable for the 'T' dimension
6344 o add CF-style coordinate variables to MNC
6345 - just a first cut: numbers are meaningless on the cubesphere and
6346 missing along the T axis but otherwise it works!
6347 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
6348 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
6349 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
6350 this is based directly on what the model compute, so that the content of
6351 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
6352 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
6353 o clean up build options files for SunOS, in particular
6354 - remove -traditional from xmakedepend
6355 - change -xarch=v9 to -xarch=native for f77
6356 - restore use of make (not gmake)
6357 - add CC=gcc if using g77
6358 o changes per discussion of AM, JMC, & EH3 today:
6359 - move redundant "grid" variables out of "state" -- in preparation of
6360 creating proper CF-style coordinate variables and in recognition
6361 that any/all grid variables can be easily copied (eg. w/NCO) from
6362 the grid files into any of the other NetCDF files
6363 - *always* output grid variables with MDSIO (this will eventually be
6364 changed)
6365 - output MNC grid file if useMNC is true
6366 o every instance of _END_MASTER() has been found and replaced with
6367 _END_MASTER( myThid ) in order to satisfy certain picky Sun
6368 preprocessors
6369 o re-arrange diagnostics pkg initialisation:
6370 - allow each package to extend the available diagnostics list
6371 - add some checking and fix small problems (multi-threaded, ...)
6372 - new S/R diagnostics_fill (replace fill_diagnostics):
6373 look through the short list of active diag. (instead of the long list)
6374 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
6375
6376 checkpoint57a_post (2004/12/10)
6377 o this set of changes restores TAMC compatibility
6378 tested for global_ocean.90x40x15 adjoint on trough
6379 (what a pain)
6380
6381 checkpoint57a_pre (2004/12/10)
6382 o some modifs in tools/build_options for sunos
6383 o call ctrl_pack for ctrl at end for optimcycle=0
6384
6385 checkpoint57 (2004/12/09)
6386 o add horizontal bi-harmonic viscosity for vertical velocity
6387 - new parameter viscA4W (defaults to viscA4)
6388 - affects only non-hydrostatic code
6389 - to be done: no-slip lateral boundary conditions
6390 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
6391 o implement Implicit Vertical advection for pTracers
6392 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
6393 (implemented also for implicit vertical diffusion & advection)
6394 o OBCS: extend application of tracer open boundary conditions
6395 to a strip beyond the boundary of width Olx/Oly
6396 o add call monitor to TAF set of required calls (flow directives)
6397 and include in natl_box_adjoint
6398 o untangle a few ifdefs related to cost, ctrl, autodiff
6399 untangel a few ALLOW_ECCO_OPTIMIZATION
6400 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
6401 (theta2, salt2 in ecco_cost_weights)
6402
6403 checkpoint56c_post (2004/12/03)
6404 o OBCS as control variables
6405 - update ctrl_ad_diff.list, obcs_ad_diff.list
6406 - remove balance of obcs controls from default
6407 - fix index bug nobcs in ctrl_init
6408 - fix dummy fields filen in ctrl_pack
6409 - add dummy weights for obcs
6410 o lsopt: comment out fort.94 output
6411 o optim:
6412 - remove unnecessary header files
6413 - adjusted namelists
6414 - add xerbla.F to Makefile
6415 o exf:
6416 - multiple modifications of exf_check_range
6417 - unit change in exf_init_runoff from [m/year] to [m/s]
6418 o mdsio:
6419 - i/o-vector change debugLevel from debLevA to debLevB
6420
6421 checkpoint56b_post (2004/12/01)
6422 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
6423 is called from DO_THE_MODEL_IO
6424 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
6425 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
6426 - clean up PTRACERS_WRITE_TIMEAVE a little
6427 o add another verification experiment that tests both the cfc-pkg and
6428 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
6429 reactive tendencies treated inline with regular timestepping
6430 o testreport previously did a lousy job of comparing small numbers, so
6431 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
6432 implemented in the little c-progam tmp_cmpnum.c which is embedded in
6433 testreport.
6434 o ptracers_monitor: bug fix for MPI
6435
6436 checkpoint56a_post (2004/11/28)
6437 o GCHEM: finish reorganizating the package
6438 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
6439 (introduces another 3D-array for each passive tracer, but only if
6440 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
6441 gchemTendency is not needed because the timestep is done separately)
6442 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
6443 - GCHEM is now---more or less cleanly---separate from PTRACERS
6444 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
6445 so clear to me how that should be done in a general way.
6446 o CFC: improve formatting of output in CFC_ATMOS
6447 o PTRACERS:
6448 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
6449 that ALL experiments with ptracers enable can be checked. This makes
6450 GCHEM_MONITOR obsolete.
6451 - include a runtime parameter PTRACERS_monitorFreq that defaults to
6452 monitorFreq
6453 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
6454 o add PTRACERS (PTR0[1-5]) to testreport output
6455 o exf_check_range:
6456 * default changed to .TRUE.
6457 * will check values for niter0 if debLevA, every timestep if debLevB
6458 * STOP in exf_check_range if 'out of range'
6459 * range chosen generous to allow for potential extema
6460 TBD: a version with stricter range
6461 permitted range would be runtime parameters
6462 o GMredi:
6463 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
6464 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
6465 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
6466 o GCHEM:
6467 - move call to GCHEM_FORCING_SEP, so that it is now called before
6468 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
6469 - introduced a useGCHEM runtime flag and applied it everywhere.
6470 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
6471 this flag is now only visible within GCHEM-pkg routines.
6472 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
6473 be replaced by a 3D array that is computed before thermodynamics; for
6474 this, the tracer ID iTracer had to be included into the parameter list
6475 of ptracers_forcing
6476 - set up forward_step to call gchem_forcing, that will replace
6477 gchem_forcing_int in ptracers_forcing
6478 - cleaning up
6479 o small cleaning of exch2: remove files that are also in eesupp/src
6480
6481 checkpoint56 (2004/11/17)
6482 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
6483 o mnc: cleanup "full" files--fixes out-of-memory problem
6484 o ECCO-GODAE
6485 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
6486 * fully merged and updated from SIO code
6487 windstress sign change affects
6488 - exf_inscal_[u/v]stress
6489 - sign of xx_tau[u/v] adjustments
6490 - signs in cost_scat
6491 * ctrl_get_gen: avoid update of tau[u/v] for first few days
6492 * natl_box_adjoint updated and compressed
6493 * 2-level checkpoint switch added
6494 (tested in EXP. 1 of natl_box_adjoint)
6495 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
6496 o SVD
6497 * first complete, non-hacked version for SVD calculations
6498 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
6499 performed via direct access files admtlm_vector.it????
6500 (via ctrl_[un]pack)
6501 * optimcycle is used for ARPACK iteration counter
6502 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
6503 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
6504 and add linear transforms where necessary
6505 * controls are initial/final SST, SSS (can be extended; need to check
6506 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
6507 o mdsio: filename info to both stderr, stdout
6508 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
6509 from sign change
6510
6511 checkpoint55j_post (2004/11/10)
6512 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
6513 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6514 o add consistent build directories and .cvsignore files to verification
6515 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
6516 o make all subroutines 30 or less characters in length for certain older
6517 compilers to work (a thorough search only turns up two routines in
6518 pkg/ptracers)
6519 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
6520 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6521
6522 checkpoint55i_post (2004/10/28)
6523 o change arrays for total vertical diffusivity (2.D if explicit,
6524 3.D if implicit) ; each ptracer uses its own background value.
6525 o added mnc/NetCDF output capability to ocn_compon_interf
6526 - added bits to verification/cpl_aim+ocn so that it can run on
6527 ITRDA and other clusters without the mpirun "-wd" option
6528 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
6529 configuration
6530 o give MNC the ability to create additional files rather than
6531 exceeding a specified file size limit "MNC_MAX_FILESIZE"
6532 - the default is just less than 2GB which is a practical limit
6533 on many systems
6534 o Compute the non-local term using either KPP vertical diffusivity (=default)
6535 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
6536
6537 checkpoint55h_post (2004/10/20)
6538 o add verification test "vermix"
6539 o remove all the *_ioinc flags and replace with the single global
6540 outputTypesInclusive flag
6541 o allow to set a vertical profile of vertical diffusivity for T & S
6542 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
6543 o useMNC moved from data.mnc to data.pkg
6544
6545 checkpoint55g_post (2004/10/14)
6546 o Renaming carbon AD experiments to comply with testreport conventions
6547 o Updating adjoint of Held-Suarez hs94.1x64x5
6548 o Fixing directives for non-ECCO forward_step, after ECCO directives
6549 have been fixed to avoid recomp. of do_oceanic_phys
6550 Works well for global_ocean.90x40x15,
6551 but recomp. issue remains for carbon
6552 o Updating adjoint output for natl_box_adjoint after
6553 pkg/ecco has been modified (see taga c55d_post)
6554
6555 checkpoint55f_post (2004/10/13)
6556 o rename to timeave_init_fixed
6557
6558 checkpoint55e_post (2004/10/13)
6559 o some delicate re-shuffle of store directives to avoid one
6560 extra call of do_oceanic_physics
6561 affects ecco_the_main_loop.F, do_oceanic_physics.F
6562 checkpoint_lev1_directives.h
6563 o NB: this may break global_ocean adjoint temporarily,
6564 but it is clear how to fix it. Will do later, need this now.
6565
6566 checkpoint55d_post (2004/10/11)
6567 o ECCO specific cost function terms (up-to-date with 1x1 runs)
6568 o ecco_cost_weights is modified to 1x1 runs
6569 o modifs to allow observations to be read in as
6570 single file or yearly files
6571 o enable to read exf forcing fields as either
6572 single file or yearly files (flag useExfYearlyFields)
6573 checkpoint55d_pre (2004/10/08)
6574
6575 o switch between 2-level and 3-level checkpointing
6576 o add ability of MNC to write local and "partial" (eg. 2D slices where
6577 the full 3D field is never actually stored) arrays to NetCDF files
6578 with the correct (that is, the complete multi-dimensional) set of
6579 array indicies
6580 - used in mom_vecinv() to write the diagFreq output
6581 - tested (demonstrated) in verification/aim.5l_cs
6582 o further mnc-ification
6583 - add verification/lab_sea to the list with mnc setups
6584 - fix undefined mnc v-names in cd_code
6585 - add kpp to mnc output (both snapshot and timeave)
6586 o non-hydrostatic code
6587 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
6588 in calc_gw.F
6589 - defaults to viscAh
6590 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
6591 friction or Leith) in non-hydrostatic mode, as long as there is
6592 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
6593 o pkg/cost
6594 extend simple cost functions to treat time mean quantities
6595 (T,U,V) via cost_accumulate_state from cost_tile
6596 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
6597 be 2 times larger than the minimum size the advection scheme requires.
6598 now get a perfect conservation of salt in advect_cs test-exp (updated)
6599 o GGL90 (Gaspar's TKE mixed layer)
6600 - add horizontal diffusion of TKE, requires exchanges in
6601 do_fields_blocking_exchanges, horizontal diffusivity is zero by
6602 default. In OPA there is no horizontal diffusion of TKE but the
6603 mixing coefficients are computed from a horizontal average of TKE of
6604 6 points or so. I think that diffusion has a little more physical
6605 justification.
6606 - clean up ggl90_calc in the hope of reducing memory usage (this hope
6607 was in vain)
6608 - mask tke-variable in ggl90_init
6609 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
6610 o fix biharmonic diffusion on CS-grid.
6611 o more obcs stuff
6612 - added obcs_external_fields_load as an alternative to the EXF-pkg option
6613 for reading boundary values. This routine is called from
6614 obcs_prescribe_read
6615 - updated obcs_check
6616 - changed sponge layer relaxation parameter units for days to seconds
6617 - turned off sponge layer by default
6618 - changed argument list of OBCS_CALC to myTime+deltaTclock
6619 - fixed about 35 bugs in obcs_external_fields_load
6620
6621 checkpoint55c_post (2004/09/23)
6622 o obcs stuff
6623 - new runtime flags useOBCSprescribe, useOBCSbalance
6624 - re-arranged obcs_calc
6625 - moved exf_getobcs to obcs_prescibe_read
6626 obcs_prescibe_read is called after ORLANSKI stuff
6627 and independent of it (executable can contain all).
6628 - updated obcs_check
6629 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
6630 These may be necessary only if tangential velocities are
6631 prescribed at OB, not sure, needs testing.
6632 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
6633 which simplifies the calls and passes the ifc check-bounds test
6634
6635 checkpoint55b_post (2004/09/22)
6636 o add a 2D scalar, Z location, exchange_2 routine.
6637 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
6638 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
6639 affects advect_cs results (for the wrong reason): update output.txt
6640 o use a more standard discretization for biharmonic viscosity ;
6641 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
6642 affects results of dome set-up: update output.txt
6643 o fix gad_advection.F (CubedSphere part), back to version 1.23
6644 o fix bug in mom_vi_del2uv.F (CubedSphere part).
6645
6646 checkpoint55a_post (2004/09/20)
6647 o merged code to
6648 * prescribe/read time-dependent open boundaries
6649 (works in conjunction with exf, cal)
6650 * sponge layer code for open boundaries
6651 * each boundary N/S/E/W now has its own CPP option
6652 (healthy for the adjoint)
6653
6654 checkpoint55 (2004/09/17)
6655 o up-to-date adjoint of previous breaks
6656 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
6657 - global_ocean_ebm: adjoint still needs fix (TLM ok)
6658 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
6659 - carbon: * remove tr1-related adjoint verification
6660 * add ptracer as control variable
6661 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
6662 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
6663
6664 checkpoint54f_post (2004/09/16)
6665 o in verification/carbin/ remove experiment related to
6666 ALLOW_PASSIVE_TRACER (array tr1 etc)
6667 code_ad/ input_ad/ results_ad
6668
6669 o add two new packages
6670 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
6671 + subject to optimization (memory)
6672 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
6673 + subject to reordering (many GOTOs in the original code)
6674 + so far opps is called for every (i,j) point, and then operates in
6675 the vertical; one may want to reorder the scheme in order operate in
6676 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
6677 fields)
6678 o overhaul of IO so that we now have flags for MDSIO and/or MNC
6679 - all verification tests compile and run with linux_ia32_g77
6680 - defaults are compatible with current input files--nothing
6681 should change if you were not previously using MNC
6682 - MNC output has been added in numerous places (eg. timeave)
6683 but there are still a few writes not yet do-able with MNC
6684 (this is in progress)
6685 - flags now allow for either/or/both use of MDSIO and MNC and
6686 documentation will soon follow
6687 - numerous small formatting cleanups for ProTeX
6688 o add version info (via BUILD_INFO.h) to MNC and stdout
6689
6690 checkpoint54e_post (2004/09/02)
6691 o add two new packages
6692 - pp81 (Packanowski and Philander, 1981), Richardson number and
6693 stratification dependent mixing
6694 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
6695 - these scheme operate in a similar manner as KPP (without ghat, of
6696 course), however there is only one diffusivity that is used for both
6697 temperature and salinity (and passive tracers)
6698 o add offline package
6699 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
6700 provided by Stephanie Dutkiewicz
6701 o genmake2: add ability to search for C compilers and cleanup test output
6702 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
6703
6704 checkpoint54d_post (2004/07/27)
6705 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
6706 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
6707 leading to additional shift by 5 days each year of integration
6708 (i.e. leading to considerable offset over the years)
6709 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
6710 o start with no AB and no initial filtering (staggerTimeStep):
6711 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
6712 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
6713 (external loading & cpl import/export stay in forward_step.F)
6714 o update coupling interface to work with new staggerTimeStep
6715 o change MDSIO ptracers_pickup.
6716 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
6717 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
6718 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
6719
6720 checkpoint54c_post (2004/07/18)
6721 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
6722 this affects (truncation error) output.txt of test-exp:
6723 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
6724 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
6725 o change Qnet to always be the net heat flux, (+upward).
6726 affects (truncation error) output of natl_box exp.: updated
6727 o define the max number of passive tracers in PTRACERS_SIZE.h
6728 o start to test mnc routinely in exp0
6729 o add sea-ice loading (sIceLoad) as a new forcing field.
6730
6731 checkpoint54b_post (2004/07/08)
6732 o add testreport "-j JOBS" option for parallel builds (tested and pretty
6733 impressive on Altix and Opteron systems)
6734 o diagnostics can now write NetCDF files through the mnc package
6735 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
6736 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
6737 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
6738 affects (truncation error) output of lab_sea & natl_box exp.: updated
6739 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
6740
6741 checkpoint54a_post (2004/07/06)
6742 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
6743 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
6744 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
6745 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
6746 + internal_wave (shift in writing cg2d_ini_res)
6747 checkpoint54a_pre (2004/07/05)
6748
6749 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
6750 - modified verification/lab_sea and natl_box_adjoint accordingly
6751
6752 checkpoint54 (2004/07/02)
6753 checkpoint53g_post (2004/07/02)
6754 o prepare splitting of thermodynamics: store convect.counter in common block
6755 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
6756 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
6757 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
6758 o new parameter "nShapS": allow to treat differently S from T (nShapT)
6759 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
6760 o restore adjointability
6761
6762 checkpoint53f_post (2004/06/25)
6763 o modifications that affect AIM experiment results (update output.txt):
6764 - no advection of S at top interface Nr (pkg/generic_advdiff)
6765 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
6766 o AIM pkg:
6767 - include stability function into surf.Flux derivative relative to Tsurf
6768 - calculate clear-sky radiation & surface temp. change (for diagnostics)
6769
6770 checkpoint53e_post
6771 o merged cylindrical coord configuration
6772 o added rotating_tank experiment
6773 checkpoint53e_pre
6774
6775 checkpoint53d_post (2004/06/14)
6776 o faulks upgraded: re-generate output.txt that have changed:
6777 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
6778 o Added Bryan and Lewis, 1979, vertical diffusivity profile
6779 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
6780 o added Sadourny discretization of Coriolis
6781 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
6782 - re-enabled use of omega3 (useAbsVorticity)
6783 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
6784 vector-invariant equations
6785 - note: does *NOT* yet use same variable visc. for no-slip BC's.
6786 o recoded the lateral boundary conditions for non-hydrostatic w, this time
6787 hopefully without new bugs
6788 - still to do: biharmonic friction for non-hydrostatic w
6789 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
6790 o regenerated output for global_ocean_ebm (using -ieee)
6791 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
6792 of mom_common/
6793 - simple re-arrangement of instructions within computing loop
6794 checkpoint53d_pre (2004/05/21)
6795
6796 checkpoint53c_post (2004/05/21)
6797 o new version of coupler for AIM+thSIce and Ocean models
6798 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
6799 - land: change Evaporation of snow
6800 - aim with thSIce: fix bug in snow-precip.
6801 o changes to calc_gw.F
6802 - bug fix for w^2 term near the bottom boundary
6803 - (hopefully) improve the lateral slip boundary condtions for use with
6804 partial/looped cells
6805 - because the bug fix changes two verification experiments anyway (exp5
6806 and plume on slope), change the lateral boundary condition from half slip
6807 to the value of no_slip_sides
6808 o ebm package wasnt quite up to the parallel task. Fixed that.
6809 o Adjoint of EBM package + verification
6810 * TLM OK
6811 * ADM not sufficient accuracy yet (needs further testing)
6812
6813 checkpoint53b_post (2004/05/14)
6814 o Commiting new energy balance model to repository
6815 * package is pkg/ebm
6816 * verif. is verification/global_ocean_ebm
6817 * references are in ebm_driver.F
6818 C * X. Wang, P. Stone and J. Marotzke, 1999:
6819 C Global thermohaline circulation. Part I:
6820 C Sensitivity to atmospheric moisture transport.
6821 C J. Climate 12(1), 71-82
6822 C * X. Wang, P. Stone and J. Marotzke, 1999:
6823 C Global thermohaline circulation. Part II:
6824 C Sensitivity with interactive transport.
6825 C J. Climate 12(1), 83-91
6826 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
6827 C Destabilization of the thermohaline circulation
6828 C by atmospheric eddy transports.
6829 C J. Climate 7(12), 1870-1882
6830 o Will need long integration testing.
6831 checkpoint53b_pre (2004/05/14)
6832
6833 o created pkg/mom_common in preparation for variable viscosity code
6834 o renamed and split ini_mnc_io
6835 o pkg/land: only liquid water can diffuse or run-off
6836 o AIM using land: soil wetness availability account for snow
6837 o added printMapIncludesZeros to EEPARMS namelist
6838
6839 checkpoint53a_post (2004/05/11)
6840 o restore TAMC compatiility for exf_constants.h
6841 (no usage of _d in .h)
6842 o Additional storing in KPP in an attempt to fix
6843 TAMC problem with adjoint of KPP code.
6844 (no success...)
6845 Identical code works fine with TAF.
6846 o Fixed verification/natl_box_adjoint experiments.
6847 Initial conditions for Experiments 4 and 5 are now
6848 set to "SEAICE_initialHEFF=0", which is more reasonable,
6849 and hence gives results closer to that of Experiment 2.
6850 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
6851
6852 checkpoint53 (2004/05/06)
6853 o stable checkpoint with up to date adjoint
6854 TLM tests only run for 1st grdchk at the moment. Its unclear if
6855 this is a code problem or a problem with resetting code for g_
6856 variables that is being autogenerated wrong.
6857 Otherwise:
6858 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
6859 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
6860 are both still in chaos following their security messes.
6861
6862 checkpoint52n_post (2004/05/06)
6863 o various build (mostly genmake2) changes including:
6864 - ability to build/run more easily within Cygwin and MacOS X
6865 - more complicated Makefiles with a stronger dependence on Gnu Make
6866 o pkg/seaice modifications
6867 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
6868 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
6869 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
6870 - changed proxy for geostrophic velocity and updated
6871 verification/lab_sea/results/* accordingly
6872 - removed ADI dynamic solver from pkg/seaice
6873 - replaced all occurrences of 1/CSTICE or 1/CSUICE
6874 they caused a segmentation fault under certain circumstances
6875 - removed unused field WATR
6876 o bug fix in exf-package:
6877 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
6878 now reflect that.
6879 o small fixes in the cal-package:
6880 - set reference date to first of January for the 'model'-calendar
6881 - failing of cal_CheckDate in cal_FullDate now actually results in a
6882 warning
6883 o small modifications in exf-package to increase flexibility:
6884 - change climtempfreeze from a constant to a runtime parameter that
6885 is specified in data.exf_clim (default = -1.9)
6886 - introduce runtime parameter windstressmax (default = 2.0) that is
6887 specified in data.exf
6888 o fix in pkg/thsice:
6889 - update Evap (Tsf changes) to be consistent with Latent heat flux
6890 - maintain snow precipitation unchanged (even if Tsf >=0).
6891 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
6892
6893 checkpoint52m_post (2004/04/18)
6894 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
6895 this does not change any of the results, because myIter=0 in swfrac always
6896 lead to jwtype=2 (the default anyway), but the call makes little sense
6897 as a default
6898 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
6899 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
6900 atmospheric model (AIM) to use it ; add a "slab ocean" component.
6901 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
6902 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
6903 o extending useSingleCpuIO option to work with new exch2 I/O format
6904 - old-style, missing-tile I/O is still accessible by defining CPP
6905 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
6906 o monitor package can write to NetCDF files and/or STDOUT
6907 o fix re-definition bug in MNC_GRID_INIT_ALL()
6908 o doc/api_reference added
6909 - a framework for building an API Reference Manual using all
6910 the "protex" comments embedded in the code
6911 - see pkg/generic_advdiff, pkg/mnc for examples
6912 o MNC:
6913 - make myThid the last argument for all subroutines
6914 - new default for the grid files: NO halos
6915 - add useMNC and other run-time flags
6916 - separate per-file-group handling of the unlimited dimension
6917 - early initialization of MNC w/ flags read at the eeboot stage
6918 and lookup tables set in initialize_fixed
6919 - write all MNC output to a freshly-created directory
6920 o thermodynamics sea-ice (thsice) is now tested with testreport.
6921 o test exp. advect_cs: use the standard cs32 grid ; update output.
6922 o Added functionality to grdchk:
6923 pick global i,j,k position (or nearest wet) where to perform check.
6924
6925 checkpoint52l_post (2004/03/11)
6926 o new land formulation:
6927 a) use ground enthalpy as prognostic variable to ensure exact
6928 energy conservation.
6929 b) account for water temperature and for latent heat of freezing
6930 in all processes (rain, run-off, ground storage)
6931 c) compute surface and ground temperature implicitly.
6932 o aim_v23 modification for new land model:
6933 a) Treat separately land / ocean / sea-ice surface fluxes
6934 to allow implicit computation of land & sea-ice surface temp.
6935 b) add snow precipitation.
6936 checkpoint52l_pre (2004/03/11)
6937
6938 o fix problem (when 1 tile is empty) in min/max monitor.
6939 o fix bug in timeAve (u,vZetatave in common block)
6940 o no restoring terms under ice for pkg/seaice
6941 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
6942 o bug fix for pkg/seaice pickups
6943 o change MNC call locations and add coordinate attributes
6944 o mask vorticity at the corner ; affects global_ocean.cs output
6945 o fix ini_curvilinear_grid ; test CS experiments with mpi
6946 o aim.5l_cs: modify sea-ice fraction input file ; update output
6947 o exf: Adding simple range check routine for exf fields after read
6948
6949 checkpoint52k_post (2004/02/23)
6950 o removed top-level directory "diags"
6951 - we migrated these functions to pkg/timeave a long time ago
6952 o fixed bug introduced in pkg/monitor
6953 o accuracy ctrlprec = 32 insuffient for gradient checks using
6954 averaged fields (I/O via cost_averages)
6955 -> use ctrl.h in active_file*.F to control I/O precision.
6956 o paramter list of CALL ADTHE_MAIN_LOOP
6957 o added initial do_the_model_io to ecco
6958 o set all ...Freq to zero after cost_final
6959 taveFreq, dumpFreq, pChkptFreq
6960 o MAIN and ECCO differentiability restored
6961
6962 checkpoint52j_post (2004/02/18)
6963 o fix nchklev in tamc.h for global_ocean...
6964 o Bringing flow and store directives up-to-date
6965 o Really weird thing!
6966 call do_the_model_io from the_main_loop with parameters
6967 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
6968 TAF places a faulty re-call of initialise_varia
6969 after cost_final call which should not be there!
6970 checkpoint52j_pre (2004/02/03)
6971
6972 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
6973 error messages
6974 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
6975 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
6976 debug output
6977 o modfied mdsio_writefield.F to handle non-global files under exch2
6978 o update AIM Cubed-Sphere exp (aim.5l_cs):
6979 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
6980 o update AIM Equatorial Channel exp:
6981 use standard aim_v23 pkg and change the SST fields to be more realistic.
6982 o globalFile now works with exch2
6983 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
6984 mon_vort3.F to make exch2 friendly with >1 tile per cube face
6985 o limit timeave output for hi-res integrations
6986
6987 checkpoint52i_post (2004/01/21)
6988 o removed CPP_EEOPTIONS.h from verification/*/code
6989 o updated the tiling for global_ocean_pressure
6990 checkpoint52i_pre (2004/01/20)
6991
6992 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
6993 the old pkg/aim).
6994
6995 checkpoint52h_pre (2004/01/20)
6996 o shortened offending lines in exch2_send_rx?.template
6997 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
6998 o genmake2: add build & execute test for NetCDF code
6999 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
7000 old grid files, moved CPP_EEMACROS.h to pkg/exch2
7001 o added useSingleCPUIO flag to monitor.F and mon_out.F
7002 o added temporary hack for sea-ice dynamics on the cube:
7003 metric terms are ignored and it is assumed that
7004 there is no sea-ice on cube faces 1, 2, 4, and 5.
7005
7006 checkpoint52f_post (2004/01/09)
7007 o added exch2 cube routines to pkg/exch2
7008 o modified hs94.cs-32x32x5 to use it
7009 o added new grid files to hs94.cs-32x32x5
7010 checkpoint52f_pre (2004/01/07)
7011
7012 checkpoint52e_post (2004/01/07)
7013 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
7014 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
7015 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
7016 to work with implicit vertical advection and AB ;
7017 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
7018 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
7019 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
7020 checkpoint52e_pre (2004/01/02)
7021
7022 o fix bug in impldiff when Nr=1 or Nr=2.
7023 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
7024 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
7025 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
7026 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
7027 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
7028 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
7029 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
7030
7031 checkpoint52d_post (2003/12/16)
7032 o re-tiled many expts to allow comparison in multi-processor mode
7033 - updated output accordingly
7034 - changed hs94.128x64x5 to use intial T from file rather than use the
7035 random number generator
7036 o add infrastructure in model routines for fizhi and gridalt packages
7037 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
7038 o changes to permit hi-res, cubed-sphere, configuration
7039 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
7040 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
7041 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
7042 of surface winds for the cube
7043 (A verification experiment, based on global_ocean.cs32x15, but with
7044 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
7045 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
7046 complete with example surface forcing files and matlab scripts to look
7047 at the output and compare it with that of global_ocean.cs32x15.)
7048 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
7049 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
7050 to conform to the common rule.
7051 o check-in the first version of the coupler + interfaces for multi-components
7052 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
7053 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
7054 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
7055 - ocean and atmos. share the same horizontal grid (no interpolation).
7056 - exchanges between component and coupler is done in forward_step
7057 o new verification experiment, cpl_aim+ocn:
7058 coupled ocean - AIM atmosphere on cs32 grid.
7059
7060 checkpoint52d_pre (2003/12/06)
7061 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
7062 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
7063
7064 checkpoint52c_post (2003/11/25)
7065 o Fixing OPTIONS files for use of exf:
7066 - ALLOW_ECCO not needed
7067 - ECCO_CPPOPTIONS.h should not be included from
7068 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
7069 as has been the case in the past
7070 - All cal/exf related options are currently set in
7071 single header file. Should remain so until we
7072 agree on a consistent new policy.
7073 o Removed all CPP options for cal package.
7074 cal has no more CPP options.
7075 o modified STOREs in GAD_ADVECTION
7076 o corrected key comp. for passkey
7077
7078 checkpoint52b_post (2003/11/23)
7079 o new version: "thsice" of thermodynamic sea-ice pkg:
7080 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
7081 - modify fluxes but do not change theta directly;
7082 - light cleaning of bulk_force pkg (still needed with thsice).
7083 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
7084 + output_thsice.txt to test thsice & bulk_force pkgs.
7085 o put back grid & coriolis monitor output.
7086 checkpoint52b_pre (2003/11/23)
7087
7088 o call "do_the_model_io" at the beginning (=> dump initial state)
7089 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
7090 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
7091 (need info on NUMBER_OF_PTRACERS)
7092 o missing PTRACERS headers in some routines
7093 o default tamc.h in pkg/autodiff supposed to crash
7094 to ensure proper customization
7095
7096 checkpoint52a_post (2003/11/17)
7097 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
7098 - moved surfaceTendencyTice from pkg/seaice to main code
7099 - subroutine FREEZE_SURFACE now limits only surface temperature
7100 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
7101 => new output.txt for global_ocean.cs32x15 & global_with_exf
7102 - keep the old version of FREEZE for backward compatibility;
7103 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
7104 - corresponding modifs for TAF directives
7105 o added surface flux output variables to TIMEAVE_STATVARS
7106 o time-averaged output for pkg/ptracers
7107 o fix problem with ECCO-related divided adjoint
7108 snapshot file was missing some ad-variables,
7109 but no warning issued by TAF
7110
7111 checkpoint52a_pre (2003/11/12)
7112 o some bug fixes for #undef REAL4_IS_SLOW
7113
7114 checkpoint52 = ecco_c52_e35
7115 o after testing adjoints of checkpoint51u_post
7116
7117 checkpoint51u_post (2003/11/06)
7118 o this is the post-merge tag of the ecco-branch
7119 (needs another clean checkout and re-testing)
7120 o various natl_box_adjoint configs and results
7121 but no input fields
7122 o obcs adjoint not yet merged!
7123 o adding ECCO global 1x1 and 2x2 degree configs
7124 o updated/extended some store directives for seaice
7125 o pkg/ecco now containes ecco-specific part of cost function
7126 o top level routines the_main_loop, forward_step
7127 supersede those in model/src/
7128 previous input data.cost now in data.ecco
7129 (new namelist ecco_cost_nml)
7130 o in ctrl/ cleaned some cross-dependencies and updated CPP options
7131
7132 checkpoint51t_post (2003/11/04)
7133 o this is the pre-merge tag of the ecco-branch
7134
7135 checkpoint51s_post (2003/11/04)
7136 o cleanup: removed various obsolete #define-s
7137 o pkg/grdchk
7138 - renamed 'ph-grd 3' to 'grad-res'
7139 - merged from ecco-branch
7140 (remaining bug fixes for obcs gradient checks)
7141 - additional high-precision output for testreport
7142 (grep for 'precision_grdchk_result')
7143
7144 checkpoint51r_post (2003/11/03)
7145 o cleaned up or removed CPP_OPTIONS.h files
7146 o updated results for some of the tests to reflect the new
7147 optfiles (-ieee: -O0 instead of -O3)
7148
7149 checkpoint51q_post (2003/10/30)
7150 o cd_code:
7151 - moved cd_scheme.F -> cd_code_scheme.F
7152 - separate read_checkpoint from cd_code_ini_vars.F
7153 - separated cd_code part from write_checkpoint
7154 - updated AD_SOURCE, generated .flow
7155 - added CD_CODE_VARS.h to the_main_loop
7156 - Moving cd_code specific store dir.s to pkg/cd_code
7157 o ctrl package totally restructured
7158 - pack/unpack now optional and decoupled from
7159 xx_/adxx_ I/O
7160 - ctrl_pack/unpack cleaned
7161 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
7162 - confined inclusion of AD_CONFIG.h to where necessary.
7163 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
7164
7165 checkpoint51p_post (2003/10/30)
7166 o create initial cd_code package
7167 - WARNING: the initialization of fields within packages
7168 is broken because INI_FIELDS (where READ_CHECKPOINT is
7169 called) is called *before* PACKAGES_INIT_VARIABLES.
7170 This seems to be backwards since
7171 1) its important to initially zero the entire field including
7172 the "halo" region
7173 2) zeroing needs to be done *before* reading pickup info
7174 and the pickup call might or might not happen in any
7175 particular run
7176 - this needs an overhaul for R2
7177 o cleanup verification/*/code/GMREDI_OPTIONS.h
7178 o cleanup testreport
7179
7180 checkpoint51o_post (2003/10/27)
7181 o bringing AD-related verif's up to date with genmake2
7182 - carbon/
7183 - global_ocean.90x40x15/
7184 - hs.94.1x64x5/
7185 - (front_relax/ )
7186 o (more) consistent directory structure for AD-related verif.'s
7187 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
7188 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
7189 o bug fix in find_alpha.F for MDJWF:
7190 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
7191 change rho -> rho-rhoConst
7192 - replace call find_rho to find_rhonum
7193 o initialisation of rFlx extended to full array (required by TAF)
7194 and shifted to thermodynamics
7195 o removed PTRACERS.h in ptracers routine
7196 o added surfacetendencyPtr to S/R parameter list pracers_forcing
7197 o Correcting initialisations for fVerU, fVerV.
7198 o helping TAF to recognize dependency on kUp for
7199 fVerU, fVerV
7200 o Replacing delZ by delR in pkg/ctrl/
7201 checkpoint51o_pre (2003/10/24)
7202
7203 o undid all of cp51 pending some cleanups and discussion
7204 o added the [#include "AD_CONFIG.h"] statement to all files that need
7205 it for adjoint/tl #defines
7206 o re-worked the build logic in genmake2 to support AD_CONFIG.h
7207 o removed tools/genmake since it no longer works
7208
7209 checkpoint51n_post (2003/10/23)
7210 o modifications to make FREEZE flux visible to pkg/kpp
7211 - moved surfaceTendencyTice from pkg/seaice to main code
7212 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
7213 - subroutine FREEZE now limits only surface temperature
7214 (this means new output.txt for global_ocean.90x40x15,
7215 global_ocean.cs32x15, and global_with_exf)
7216 o added surface flux output variables to TIMEAVE_STATVARS
7217
7218 checkpoint51n_pre (2003/10/23)
7219 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
7220 o added [#include "AD_CONFIG.h"] to all files that use the following
7221 defines:
7222 - ALLOW_ADJOINT_RUN
7223 - ALLOW_TANGENTLINEAR_RUN
7224 - ALLOW_ECCO_OPTIMIZATION
7225
7226 checkpoint51m_post (2003/10/21)
7227 o incorporating changes to get TAMC/TAF working in genmake2
7228 - added new TAMC/TAF targets to the Makefile
7229 - various cleanups related to package handling
7230 - these changes should have no impact on the forward model
7231
7232 checkpoint51l_post (2003/10/20)
7233 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
7234 - faster algorithm for cal_addtime.F
7235 - higher precision arithmetic, where needed
7236 - pkg/exf *startdate variables changed from calendar date to
7237 model integration time
7238
7239 checkpoint51l_pre (2003/10/17)
7240 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
7241 o enable to apply restoring on S & T only in a latitude band.
7242 o update output (external_forcing_surf modif. change truncation errors)
7243 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
7244
7245 checkpoint51k_post (2003/10/16)
7246 o change default to: useNHMTerms=.FALSE.
7247 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
7248 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
7249 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
7250 exp1, ideal_2D_oce
7251 - change data file of oceanic exp (leave the results unchanged for now)
7252 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
7253 o set gravitySign automatically according to the vertical coordinate used
7254 (and change sign: back to "logical" value: +1 when R increases downward)
7255 o added an include barrier to the default CPP_OPTIONS.h and
7256 removed the #include "PACKAGES_CONFIG.h" from it
7257 o fix a bug in mom_fluxform (from chk51j_post)
7258
7259 checkpoint51j_post (2003/10/10)
7260 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
7261 o adjusted some flow directives (dynamics, thermodynamics)
7262 o added cubed-sphere case to test cost function
7263 o heckpoint_lev?_directives.h now include
7264 pkg-specific directives, whenever those are enabled.
7265 o Moving pkg-specific flow directives to corresponding pkg
7266 Moving pkg-specific differentiation list to corresponding pkg
7267 Moving pkg-specific checkpoint-lev storing to corresponding pkg
7268 ---> conventions are
7269 - pkg_ad.flow
7270 - pkg_ad_diff.list
7271 - pkg_ad_check_lev?_dir.h
7272
7273 checkpoint51i_post (2003/10/09)
7274 o merge of the branch-genmake2
7275 - knowingly breaks the older genmake
7276 - automatic generation of all ALLOW_${PKG_NAME} defines
7277 - new testreport supersedes older testscript
7278 o large number of package inclusion and header cleanups
7279 checkpoint51i_pre (2003/10/08)
7280
7281 o new output for adjoin of global ocean vector invariant
7282 o fix for checkpoint of thermodynamic seaice and bulk_force
7283 o Steph gchem various cleanups
7284
7285 checkpoint 51h_pre
7286 o fixed some single quotes
7287 o modify gchem pkg to be more versatile
7288 o modifications to clean up dic pkg
7289 o add pkg/cfc
7290
7291 checkpoint51g_post (2003/10/02)
7292 o provide links for ARPACK and ADM*TLM
7293 o start removing verification/vero/
7294 o update AD-related stuff
7295 (in particular some IF-statements in model/src/ routines)
7296 o adding to verification/global_ocean.90x40x15/ adjoint of
7297 vector invariant setup
7298
7299 checkpoint51f_post (2003/10/02)
7300 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
7301 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
7302 of tracer Green's fucntions for ocean inversion project.
7303
7304 checkpoint51f_pre (2003/08/07)
7305 o Added on-the-fly spatial interpolation capability
7306 "USE_EXF_INTERPOLATION" to pkg/exf.
7307 - This is a temporary Cartesian-grid hack until
7308 the super-duper ESMF coupler becomes available.
7309 - See verification/global_with_exf/README for usage example.
7310 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
7311 flags and modified pkg/seaice accordingly.
7312 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
7313 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
7314 non-local transport term.
7315
7316 checkpoint51e_post (2003/08/03)
7317 o pkg/mom_vecinv:
7318 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
7319 - add time-ave diagnostic of vorticity advection.
7320 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
7321 o atmospheric geopotential: - include water vapor effect;
7322 - use p^kappa in p* scaling.
7323 o land pkg: read initial state from files.
7324 o AIM : add stratospheric drag in the upper level
7325
7326 checkpoint51d_post (2003/07/18)
7327 o change function ILNBLNK (=> last non-blank char.) to return zero
7328 (instead of the string length) when the string. char is empty
7329 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
7330 o modif's to restore TAMC compatibility
7331 - avoid "_d" constructs in PARAMETER declarations
7332 - avoid interrupting lines by comment lines
7333 o Use cluster local disks for purely local I/O
7334 vs. globally visible disks needed for ctrl stuff
7335 (merged from ecco-branch)
7336 - new active_file_loc... and mdsio_..._loc routines
7337 - affected packages: autodiff, ctrl, grdchk, mdsio
7338
7339 checkpoint51c_post (2003/07/08)
7340 o introducing integer flag debugLevel
7341 - debLevZero: suppress all output
7342 - debLevA: standard
7343 - debLevB: equivalent to current debugMode=.TRUE.
7344 o introducing pathname variable mdsioLocalDir for mdsio
7345 that can be specified at runtime
7346 (relevant for cluster I/O to local disk)
7347 `
7348 >>>checkpoint51b_post
7349 adjoint of ptracers
7350 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
7351 o extended state in checkpoint_lev?, etc.
7352 o alternative ctrl/cost with tr1 or ptracer
7353 o new comlev1_bibj_ptracers
7354 o new ptracers.flow
7355 o made ptracers_forcing same as external_forcing_s
7356 o added verification for adjoint with ptracers
7357 - adm. grdchk fail so far
7358 - tlm. grdchk OK
7359 - checked tapelev/comlev recomputations: OK
7360 <<<checkpoint51b_pre
7361
7362 checkpoint51a_post (2003/06/25)
7363 o added code for biogeochemistry package
7364 - new pkgs: dic, gchem
7365 - new subroutine in ptracers
7366 o modify code for biogeo packages
7367 - in model/src and pkg/ptracers
7368
7369 checkpoint51 (2003/06/24)
7370 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
7371 - autodiff, ctrl, exf, grdchk, seaice
7372 kept separate packages
7373 - cost, ecco, obcs
7374 o updating verification/internal_wave, verification/lab_sea
7375 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
7376
7377 checkpoint50i_post (2003/06/23)
7378 o Preparing next differentiable checkpoint and sync
7379 of MAIN vs. ecco-branch
7380 - 1st step: this one is differentiable
7381 - 2nd step: next(! not this) checkpoint will have updated packages
7382 from ecco-branch)
7383
7384 checkpoint50h_post (2003/06/20)
7385 o new package "land": provide surface BC for AIM.
7386 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
7387 o AIM: use true log-P extrapolation for near surface temp (= as in
7388 F.Molteni paper) ; update aim.5l_cs output.
7389 o New variable in PARM03 for more flexible pickups
7390 o somewhat cleaned package initialisation sequence for
7391 ctrl/ cost/ ecco/ in packages_... routines
7392
7393 checkpoint50g_post (2003/05/23)
7394 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
7395 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
7396 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
7397 made the default because of faster convergence than ADI
7398
7399 checkpoint50f_post (2003/05/23)
7400 o exf totally restructured
7401 - replaced all exf_set_ routines by one generic exf_set_gen.F
7402 and made sure it's still differentiable
7403 - split exf_getffields.F into new exf_bulkformulae.F
7404 - exf_inscal_/exf_outscal_ suffixes consistent with field names
7405 - updated adjoint/makefile and relevant verif. accordingly
7406
7407 checkpoint50f_pre (2003/05/23)
7408 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
7409 + change Evap over land. (update aim.5l_cs output)
7410 o added missing .cvsignores and made uniform across expts
7411 o changed configuration of tidal_basin_2d expt
7412 o added pkg/debug functions for tracing code in fatal crashes
7413 o tidied pkg/monitor to use MONITOR_OPTIONS.h
7414 o new fn in pkg/monitor to stop model if solution grows too big
7415 o removed lots of single quotes from comments
7416
7417 checkpoint50e_post (2003/05/14)
7418 o make KPP work with PTRACERS
7419 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
7420 nearly a copy of kpp_transport_s
7421 - there is no analogue to SurfaceTendencyS, so I have to use
7422 gPtr(of the surface layer) instead
7423 o add a new platform SunFire+mpi (SunFire 15000) to genmake
7424 checkpoint50e_pre (2003/05/13)
7425
7426 checkpoint50d_post (2003/05/13)
7427 o change kpp output from multiple-record state files to single-record state
7428 files analogous to write_state.F
7429 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
7430 analogous to the cg2d-related output.
7431 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
7432 so that writing to internal file fn (with length 512) fails.
7433 checkpoint50d_pre (2003/05/12)
7434
7435 checkpoint50c_post (2003/05/12)
7436 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
7437 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
7438 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
7439 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
7440 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
7441
7442 checkpoint50c_pre (2003/04/30)
7443 Merging from release1_p13:
7444 o bug fix for pkg/seaice dynamic solver
7445 o Added SEAICE_initialHEFF to pkg/seaice
7446
7447 checkpoint50b_post (2003/04/17)
7448 o store u*,v* in gU,V instead of in guNm1,gvNm1
7449 o in order to put the momForcing out of the Adams-Bashforth:
7450 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
7451 to timestep.F
7452 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
7453 o re-generate output for highly sensitive test-exp:
7454 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
7455
7456 checkpoint50b_pre (2003/04/17)
7457 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
7458 o corrected CPP option mismatch in exf_Bulk... functions for case
7459 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
7460
7461 checkpoint50a_post (2003/03/21)
7462 o Bug fix for merging between c50 and KPP.
7463 ikey was passed from thermodynamics to kpp_calc via
7464 common block rather than being recomputed in kpp_calc,
7465 in contradiction with new key itdkey.
7466 New key ikppkey created, and tamc.h headers updated.
7467
7468 checkpoint50 (2003/03/08)
7469 - 2nd step of merge with ecco-branch:
7470 merge changes in ecco-branch back into main trunk
7471 - bug fix in find_alpha
7472 - more storing in gmredi_calc_tensor.F, kpp_routines.F
7473 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
7474 - merged some sliced AD support routines
7475
7476 checkpoint49 (2003/03/06)
7477 merged from ecco-branch:
7478 o exf:
7479 - Enable initialisation of forcing fields to constant
7480 (runtime) values.
7481 - in exf_getffields.F
7482 Reduce i-/j-loop to interior domain, discarding overlaps.
7483 That also fixes wrong TAF-key computations for key_1, key_2
7484 with bulf formulae.
7485 - exf_init.F modify #ifdef for exf_init_evap
7486 - exf_getffieldrec.F, ctrl_getrec.F
7487 The following INT-usages are not safe:
7488 fldsecs = int(fldsecs/fldperiod)*fldperiod
7489 fldcount = int(fldsecs/fldperiod) + 1
7490 and were modified.
7491 o autodiff: checkpoint_lev...
7492 - updated storing for bulk formulae (some arrays were missing)
7493 - added state for seaice package
7494 - synchronized with main branch
7495 o DIVA:
7496 Modif.s in
7497 - the_main_loop.F
7498 - the_model_main.F
7499 and added cost_final_restore.F cost_final_store.F
7500 o With these changes, it is possible to fully separate
7501 the first forward run to compute the cost function (mdthe_main_loop)
7502 and adjoint runs over individual DIVA intervals (adthe_main_loop)
7503 into separate model executions.
7504 This enables better tuning of DIVA to given queue sizes.
7505 o Loss of cost function value in consecutive DIVA runs is
7506 fixed by storing to 'costfinal' file.
7507 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
7508 beginning/end of adjoint integration is accounted for.
7509 The current changes apply to TAF-1.4.26.
7510 TAF has one remaining bug, requiring one manual change
7511 (see MITgcm manual).
7512 o cal: synchronized between MAIN and ecco-branch
7513
7514 checkpoint48i_post (2003/03/05)
7515 o Changes to restore differentiability of code w.r.t. previous tag
7516 (mostly adding new routines to make list and replacing
7517 pressure by totPhiHyd).
7518 o Updated and merged grdchk package
7519 - has both ADM and TLM checks
7520 - works for single- and multi-proc.
7521 - output cleaned
7522 - worked successfully for parallel DIVA
7523 o genmake:
7524 - Adding -platform=SP4
7525 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
7526 o Modif. for DIVA:
7527 ctrl_unpack should not be called in intermediate DIVA interval.
7528 (similar thing would apply for active files such as
7529 tbar, sbar, psbar, which should not be reinitialised;
7530 only relevant for ecco-branch)
7531
7532 checkpoint48h_post (2003/02/28)
7533 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
7534 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
7535 o Added SEAICE_initialHEFF to pkg/seaice
7536 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
7537
7538 checkpoint48g_post (2003/02/18)
7539 --- EOS:
7540 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
7541 store total Potential in totPhyHyd for diagnostics & EOS.
7542 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
7543 --- Pressure/geopotential gradient:
7544 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
7545 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
7546 ( changes results of global_ocean_pressure )
7547 o NLFS + z-coord.: add eta*Rho' contribution.
7548 o accurate phiHyd when using interface-W at the middle between 2 centers
7549 ( changes results of ideal_2D_oce )
7550 o includes r* 2nd term in potential gradient.
7551
7552 checkpoint48f_post (2003/02/18)
7553 Merging from release1_p12:
7554 o Modifications for using pkg/exf with pkg/seaice
7555 - improved description of the various forcing configurations
7556 - added basic radiation bulk formulae to pkg/exf
7557 - units/sign fix for evap computation in exf_getffields.F
7558 - updated verification/global_with_exf/results/output.txt
7559 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
7560 (SBO) core products, including oceanic mass, center-of-mass,
7561 angular, and bottom pressure (see pkg/sbo/README.sbo).
7562 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
7563 to avoid negative values in shallow regions.
7564 - updated verification/natl_box/results/output.txt
7565 - updated verification/lab_sea/results/output.txt
7566 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
7567 o Added useSingleCpuIO option (see PARAMS.h).
7568 o Updated useSingleCpuIO option in mdsio_writefield.F to
7569 work with multi-field files, e.g., for single-file pickup.
7570 o pkg/seaice:
7571 - bug fix in growth.F: QNET for no shortwave case
7572 - added HeffFile for specifying initial sea-ice thickness
7573 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
7574 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
7575 kpp_transport_t.F, forward_step.F, and the_main_loop.F
7576 o pkg/seaice:
7577 - adjoint-friendly modifications
7578 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
7579
7580 checkpoint48e_post (2003/02/12)
7581 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
7582 o dynamics: change definition of computational domain & adapt mom_fluxform
7583 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
7584 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
7585 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
7586 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
7587 global_ocean.90x40x15 global_with_exf global_ocean_pressure
7588 inverted_barometer solid-body.cs-32x32x1
7589 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
7590
7591 checkpoint48d_post (2003/02/09)
7592 o in preparation for r*:
7593 a) use pre-computed gradient of hydrostatic potential:
7594 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
7595 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
7596 => affects results of glob_oce_pressure (different truncation error)
7597 update output.txt of ideal_2D_oce & global_ocean_pressure
7598
7599 checkpoint48d_pre (2003/02/08)
7600 o in preparation for r*:
7601 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
7602 pass the 2 comp. of the grad. as arguments to momentum S/R.
7603 but for the moment, only used if it does not change the results.
7604 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
7605
7606 checkpoint48c_post (2003/02/06)
7607 Modifications in treatment of initial flux forcing controls
7608 to avoid extra storing of flux fields.
7609
7610 checkpoint48c_pre (2003/01/21)
7611 o Added tidal_basin_2d experiment (currently 1D!)
7612 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
7613
7614 checkpoint48b_post (2003/01/27)
7615 o r* coordinate added in #ifdef NONLIN_FRSURF block.
7616 (modification to pressure gradient not yet implemented)
7617 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
7618 (for U & V) that are used for vertical advection of momentum.
7619
7620 checkpoint48a_post (2003/01/24)
7621 o In preparation for r*, use temp. array to compute vertical transport
7622 in flux-form momentum pkg. => change results of few test-exp.
7623 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
7624 lab_sea, natl_box & plume_on_slope
7625
7626 checkpoint48 (2003/01/23)
7627 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
7628
7629 checkpoint47j_post (2003/01/21)
7630 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
7631 o moved adexch from forward_step to addummy_in_stepping
7632 o added exch in ctrl_map_...
7633 o aveFreq.=0. at end of cost_final to avoid overwrite in
7634 reverse checkpointing loop
7635 o Yet more changes in gmredi:
7636 * adgmredi_calc_tensor
7637 avoiding all recomputation of gmredi_slope_limit
7638 * adgmredi_x/y/rtransport
7639 added flag for excessive storing to avoid recomp. of
7640 u/v/rtans, dTdx/y/z
7641 -> this is not really necessary and very memory-consuming
7642 * adgmredi_slope_psi:
7643 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
7644 * gmredi_slope_limit
7645 re-activated full calculation of taperfct for case 'ac02'
7646 o updating verification/ adjoints of carbon, global_ocean.90x40x15
7647
7648 checkpoint47i_post (2003/01/13)
7649 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
7650 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
7651 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
7652 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
7653 o gmredi: fix few bugs.
7654
7655 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
7656 This will be a good checkpoint to plug into the ecco-branch.
7657 o few modif.'s to get latest version adjointed
7658 (mainly kick out code in ini_linear_phisurf)
7659 o modif's to run adjoint with exactConserv
7660 o case GM_BOLUS_ADVEC should be cleaned
7661 S/R gmredi_slope_psi should be cleaned
7662 o verification/carbon now has exactConserv=.TRUE.
7663
7664 checkpoint47g_post (2003/01/10)
7665 o time-average AIM output: becomes independent from statvars time-average
7666 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
7667 o After TAF bug fix:
7668 Tested adjoint of gmredi package.
7669 Tests were done with checkpoint47 rather than with latest
7670 checkpoint47f_post since the latter is broken for the adjoint
7671 verification/carbon/ contains both ADM and TLM gradient checks.
7672 Here they are, before they get changed/lost/stolen.
7673 Mostly modif.'s to fix numerical sensitivities.
7674 Gradient checks OK for
7675 - GM_taper_scheme:
7676 * clipping
7677 * ac02
7678 * linear
7679 * glw91
7680 * dm95
7681 * ldd97
7682 - GMREDI_OPTIONS:
7683 * GM_VISBECK_VARIABLE_K
7684 * GM_NON_UNITY_DIAGONAL
7685 * GM_EXTRA_DIAGONAL
7686 * GM_BOLUS_ADVEC
7687 in conjunction with data.gmredi parameters to be checked in
7688 in a few minutes under verification/carbon/code/
7689
7690 checkpoint47f_post (2002/12/28)
7691 Merging from release1_p10:
7692 o modifications for using pkg/exf with pkg/seaice
7693 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
7694 and SEAICE_EXTERNAL_FLUXES
7695 - pkg/exf CPP options EXF_READ_EVAP and
7696 EXF_NO_BULK_COMPUTATIONS
7697 - usage examples are Experiments 8 and 9 in
7698 verification/lab_sea/README
7699 - verification/lab_sea default experiment now uses
7700 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
7701
7702 checkpoint47e_post (2002/12/27)
7703 o created a tag prior to creating a branch
7704
7705 checkpoint47d_post (2002/12/16)
7706 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
7707 at the bottom boundary had an erroneous half slip boundary condition
7708 o added bottom drag and no slip boundary condition capabilities to
7709 oceanic pressure coordinates code
7710 o added new verification experiment global_ocean_pressure, this experiment is
7711 also described in the tutorial section of the manual
7712 checkpoint47d_pre (2002/12/16)
7713
7714 checkpoint47c_post (2002/12/16)
7715 o Added a verification experiment for a global cubed-sphere ocean run
7716 - verification/global_ocean.cubed32x32x30
7717 - uses pkg/therm_seaice and pkg/bulk_forcing
7718
7719 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
7720 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
7721 when using P-coordinate; only implemented for atmospheric config.
7722 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
7723 NOTES: requires option NONLIN_FRSURF to be "#define".
7724 o update advect_xz/results/output.txt (left from checkpoint44g_post)
7725
7726 checkpoint47b_post (2002/12/05)
7727 Merging from release1_p9:
7728 o pkg/seaice
7729 - removed GOTO's and added taf directives
7730 - double precision constants to reduce the g77 (Linux)
7731 to F77 (SGI) differences reported in release1_p8
7732 o tools/genmake
7733 - added SGI options
7734 o verification/testscript
7735 - updated to that of checkpoint47a_post
7736 o verification/global_ocean.90x40x15/input/eedata
7737 - modified for SGI f77 compatibility
7738 o verification/lab_sea
7739 - added description of sea-ice model
7740 - added missing matlab routines
7741 - added test of thermodynamics parallelization
7742
7743 checkpoint47a_post (2002/11/23)
7744 o new pkg: aim_v23
7745 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
7746 for now, keep the same surface forcing as before.
7747 - Part-Cell implemented into AIM; check that Heat & Water are conserved
7748 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
7749 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
7750 o add diagnostic of surface correction term in monitor output
7751
7752 o bulk_force and therm_seaice
7753 - Two packages: bulk_force (Bulk forcing)
7754 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
7755 - Earlier integration from Stephaine Dutkiewicz
7756 and Patrick Heimbach.
7757 - Two ifdef statements for compile time,
7758 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
7759
7760 checkpoint47 (2002/11/15)
7761 differentiable version of checkpoint46n_post
7762 o bug fix in quasihydrostaticterms
7763 o * "clean" adjoint code (in terms of extensive recomputations)
7764 can now be obtained for all GMREDI options (i.e. for
7765 - GM_VISBECK_VARIABLE_K
7766 - GM_NON_UNITY_DIAGONAL
7767 - GM_EXTRA_DIAGONAL
7768 - GM_BOLUS_ADVEC )
7769 * However, wrong gradient check problem remains unsolved.
7770 * New CPP options have been introduced for different
7771 tapering schemes
7772 o external_fields_load now part of differentiation list
7773 o pressure needs multiple storing;
7774 would be nice to have store_pressure at beginning or
7775 end of forward_step, e.g. by having phiHyd global (5-dim.)
7776 (NB: pressure is needed for certain cases in find_rho,
7777 which is also invoked through convective_adjustment).
7778 o recomputations in find_rho for cases
7779 'JMD95'/'UNESCO' or 'MDJWF' are OK.
7780 o #define ATMOSPHERIC_LOADING should be differentiable
7781 o ini_forcing shifted to begining of initialise_varia
7782 o Incorporating QNVS line search routines into MITgcm
7783 (this is separate code, and therefore not under pkg)
7784 lsopt/, optim/
7785 o Updated verification/carbon/
7786 - #define GM_VISBECK_VARIABLE_K
7787 - GM_taper_scheme = 'ldd97'
7788
7789 checkpoint46n_post (2002/11/12)
7790 Merging from release1_p8:
7791 o verification/natl_box:
7792 updating new external_fields_load routine
7793 o New package: pkg/seaice
7794 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
7795 The sea-ice code is based on Hibler (1979-1980).
7796 Two sea-ice dynamic solvers, ADI and LSR, are included.
7797 In addition to computing prognostic sea-ice variables and diagnosing
7798 the forcing/external data fields that drive the ocean model,
7799 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
7800 The implied surface heat flux is then stored in variable
7801 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
7802 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
7803 non-local transport term. Because this call precedes model
7804 thermodynamics, temperature under sea-ice may not be "exactly" at
7805 the freezing point by the time theta is dumped or time-averaged.
7806 N.B.: fairly large differences in accuracy occur across
7807 different platforms/compilers; comparison between
7808 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
7809 generated output gives:
7810 T S U V
7811 C D M c m s m s m s m s
7812 n p a R g m m e . m m e . m m e . m m e .
7813 f n k u 2 i a a d i a a d i a a d i a a d
7814 g d e n d n x n . n x n . n x n . n x n .
7815
7816 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
7817 o GAD:
7818 - generated new common blocks to account for call of
7819 same gad routines with differing traceridentities
7820 (needed to modify tracerIdentity indices in GAD.h)
7821 - generated separate common blocks for case useCubedSphereExchange
7822 (Department of Futurology)
7823 - parameter lists to gmredi_?transport: added tracerIdentity
7824 - added new key indices to tamc.h
7825 o external_fields_load:
7826 - added this routine to TAF list
7827 - needed to make some common blocks global and additional storing
7828 along the same lines as exf package (checkpoint_lev?_directives.h)
7829 o exf:
7830 updated external forcing package
7831 - bug fixes carried over from ecco-branch
7832 (missing OBCS_OPTIONS.h in two routines)
7833 - enable easy to use "no forcing".
7834 - added exf I/O for atmospheric loading
7835 - added exf I/O for runoff data
7836 - transfered scaling between exf <-> MITgcm to exf namelist
7837 o Adding new verification experiment global_with_exf.
7838 This verification experiment is almost identical to the
7839 global_ocean.90x40x15 experiment, except that it uses
7840 the exf (and cal) package instead of the
7841 external_fields_load routine (cf README file).
7842
7843 checkpoint46m_post (2002/11/07)
7844 o modified testscript to return -- when there are no lines of "%MON" output
7845 o added new flag "quasiHydrostatic" for QH mode
7846 and new routine quasihydrostaticterms()
7847 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
7848 New routine: mom_u_coriolis_nh()
7849 o fixed sign of non-hydrostatic metric terms in u and v equations.
7850 Depend on correct sign of gravitySign.
7851 o added work.pc* to .cvsignore in aim directories using ifc
7852 o introduced flag for controllin non-hydrostatic metric terms
7853 o removed gravitySign from PARM04
7854 o switched to g77/ifc from pgf77 in aim experiments
7855
7856 checkpoint46l_post (2002/11/01)
7857 o made convective adjustment work with pressure coordinates:
7858 - changed the direction of k-loop in convective_adjustment.F for the
7859 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
7860 - adjusted the reference pressure k-index in convective_adjustment.F
7861 - adjusted the convection condition in convect.F (in analogy to
7862 calc_ivdc.F)
7863 - convective_adjustment no longer computes anything on the halos
7864 - removed the warnings about negative salinity from find_rho.F and
7865 find_alpha.F; instead the new routine look_for_neg_salinity, called
7866 at the beginning of find_rho, find_alpha, and find_beta, does a
7867 check of the entire slice, if CPP-option
7868 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
7869 checkpoint46l_pre (2002/10/23)
7870
7871 checkpoint46k_post (2002/10/23)
7872 o fixed the verification/global_ocean.90x40x15 experiment:
7873 - new bathymetry (the world according to A., JMC, and M.)
7874 - new initial fields and forcing fields (*.bin files)
7875 - new POLY3.COEFFS (for the next release one should switch to a full
7876 equation of state: JMD95P or MDJWF)
7877 - fixed several errors and redundancies in the data file
7878 - experiment uses looped cells
7879 - added matlab directory with diagnostic scripts for plotting of output
7880
7881 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
7882 - read AIM physics parameters from a file (data.aimphys)
7883 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
7884
7885 checkpoint46j_post (2002/10/07)
7886 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
7887 o move wVel computation at the end of the time step, in S/R integr_continuity
7888 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
7889 o update timeave pkg for wVel diagnostic.
7890 checkpoint46j_pre (2002/09/27)
7891
7892 checkpoint46i_post (2002/09/25)
7893 o Clean up AIM package (and keep the results unchanged):
7894 include CPP_OPTION and use IMPLICT NONE in all routines ;
7895 declare all the variables _RL ; use _d 0 for all numerical constants.
7896 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
7897
7898 checkpoint46h_post (2002/09/25)
7899 o cleaned up the use of rhoNil and rhoConst.
7900 - rhoNil should only appear in the LINEAR equation of state, everywhere
7901 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
7902 and the dynamical equations are all divided by rhoConst
7903 o introduced new parameter rhoConstFresh, a reference density of fresh
7904 water, to remove the fresh water flux's dependence on rhoNil. The default
7905 value is 999.8 kg/m^3
7906 o cleanup up external_forcing.F and external_forcing_surf.F
7907 - can now be used by both OCEANIC and OCEANICP
7908 checkpoint46h_pre (2002/09/18)
7909
7910 Added code to convert surface volume flux (fresh water) into
7911 a mass flux when using P coordinates in the ocean (OCEANICP).
7912 Note: It assumes you have set rho0=rhoConst=density of fresh water.
7913
7914 checkpoint46g_post (2002/09/18)
7915 o Include a new diagnostic variable phiHydLow for the ocean model
7916 - in z-coordinates, it is the bottom pressure anomaly
7917 - in p-coordinates, it is the sea surface elevation
7918 - in both cases, these variable have global drift, reflecting the mass
7919 drift in z-coordinates and the volume drift in p-coordinates
7920 - included time averaging for phiHydLow, be aware of the drift!
7921 o depth-dependent computation of Bo_surf for pressure coordinates
7922 in the ocean (buoyancyRelation='OCEANICP')
7923 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
7924 Theta, Salinity, and Pressure in the parameter list. This routine is
7925 presently contained in find_rho.F. This routine does not give the
7926 correct density for 'POLY3', which would be a z-dependent reference
7927 density.
7928 o cleaned up find_rho
7929 - removed obsolete 'eqn' from the parameter list.
7930 o added two new verification experiments: gop and goz
7931 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
7932 checkpoint46g_pre (2002/09/16)
7933
7934 checkpoint46f_post (2002/09/16)
7935 o Enable tangent linear (forward mode) gradient checks:
7936 - extended active file handling to g_... files
7937 - added TANGENT_SIMULATION to theSimulationMode
7938 - extended grdchk package accordingly
7939 o added tangent linear setup in verification/carbon/code_ftl
7940 o added adjoint setup in verification/front_relax/code_ad
7941
7942 checkpoint46e_post (2002/09/05)
7943 o Added new equation of state -> MDJWF
7944 - EOS of McDougall et al., 2002, JAOT, submitted
7945 - caveat: the equation of state is only valid for a smaller (more
7946 realistic?) range of values than JMD95P/Z and UNESCO
7947 - added masks to the calculation of pressure in store_pressure
7948 - added more check values for density in check_eos (ini_eos.F), some of
7949 the old check values are out of the range of the MDJWF-eos, so don't
7950 expect perfect matches for those
7951 checkpoint46e_pre (2002/08/19)
7952
7953 checkpoint46d_post (2002/08/19)
7954 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
7955 'OCEANICP', also initialised field pressure correctly in ini_eos in the
7956 case of pressure coordinates. eosType='JMD95Z' in
7957 combination with buoyancyRelation='OCEANICP' now causes an error.
7958 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7959 in find_alpha/beta.
7960 checkpoint46d_pre (2002/08/15)
7961
7962 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7963 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
7964
7965 checkpoint46c_post (2002/08/15)
7966 o Changes necessary for ocean in p-coordinates
7967 - Added new buoyancy relation = 'OCEANICP'
7968 - Added new parameters = gravitySign (this used to be contained inside
7969 the factor dRdZ which I added when we first switched to R coordinates).
7970 X GM/Redi is not compatible (yet)
7971 X bottom drag and no-slip need to be debugged.
7972 checkpoint46c_pre (2002/08/07)
7973
7974 checkpoint46b_post (2002/08/07)
7975 o Added new equation of state -> JMD95Z and JMD95P
7976 - EOS of Jackett and McDougall, 1995, JAOT
7977 - moved all EOS parameters into EOS.h
7978 - new routines ini_eos.F, store_pressure.F
7979 o Added UNESCO EOS, but not recommended because it requires
7980 in-situ temperature (see JMD95)
7981 o Modified formatting for knudsen2.f in utils/knudsen2 and added
7982 unesco.f to be used with POLY3
7983 checkpoint46b_pre (2002/07/31)
7984
7985 checkpoint46a_post (2002/07/31)
7986 o Added (atmospheric) pressure loading
7987 - new field in FFIELDS.h, etc...
7988 - new cpp flag ATMOSPHERIC_LOADING
7989 o Changed hFacC to _hFacC in calc_phi_hyd.F
7990 o Added SHORTWAVE_HEATING to some files for consistency
7991 checkpoint46a_pre (2002/07/13)
7992
7993 checkpoint46 (2002/07/13)
7994 further merges from release1_p5
7995 o new ctrl package
7996 - adopted from ECCO environment to enable optimization
7997 - added Eliassen Palm fluxes to controls
7998 o added Eliassen Palm flux controls to gradient check package
7999 o cost package
8000 - Compatible with new ctrl package
8001 - added Eliassen Palm cost hooks
8002 - modif's of existing cost functions
8003 o Adjoint-related bug fixes in kpp:
8004 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
8005 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
8006 o autodiff package
8007 - flow directives:
8008 + new for S/R do_the_model_io
8009 + enhanced for S/R checkpoint
8010 + new gmredi.flow
8011 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
8012 disable adcommon.h/g_common.h by default.
8013 - fixed problem for adjoint of global_max
8014 o modified verification/carbon/
8015 o New setup for adjoint of global_ocean
8016 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
8017 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
8018 o incorporated hooks for sponge layer code (external_forcing.F)
8019
8020 checkpoint45d_post (2002/07/12)
8021 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
8022 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
8023 (affects plume_on_slope "cg2d" output)
8024 o add new parameter deltaTfreesurf for free-surface time stepping
8025 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
8026 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
8027 o change phiMin in exp1 (to agree with documentation)
8028 o add new flags:
8029 - T,S forcing inside/outside Adams-Bashforth
8030 - turn off temp,salt advection and/or forcing
8031 - for each tracer, define internal flag for multiDimAdvection & A-B
8032 o monitor: change definition of KE to check conservation of Energy
8033
8034 checkpoint45c_post (2002/05/30)
8035 o Removed f90 comments ("!")
8036 o Modified initialisations to enable exf package for MITgcm
8037 (without invoking ECCO_PACKAGE).
8038 o modifications to gradient check package (Martin Losch)
8039 - enable centered differences
8040 - modified format of standard output
8041
8042 checkpoint45b_post (2002/05/30)
8043 o cleaned exchange calls in cg2d
8044 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
8045 o included CPP option SINGLE_LAYER_MODE in thermodynamics
8046 to configure barotropic setup (Martin Losch)
8047 o moved some initialisations within bi,bj loop in dynamics
8048 (TAF flow dependency)
8049 o in initialise_varia, moved call packages_init_variables
8050 before convective_adjustment_init
8051 (corresponding adjustment of TAF tape initialisation).
8052 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
8053
8054 checkpoint45a_post (2002/05/01)
8055 o compute Rho over the whole domain (extend iMin,jMin indices)
8056 o specific exchange for X-slice domain (case Ny=1)
8057 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
8058 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
8059
8060 checkpoint44h_post = checkpoint45
8061 o Fix to restore differentiability:
8062 place at which packages_init_variables is called in
8063 initialise_varia is crucial for reverse control flow.
8064 o modifications in GMRedi to enable stable adjoint
8065 (corresponding modif's in thermodynamics, dynamics)
8066 o added missing hook for sponge layer code in external_forcing
8067 o modified test cost functions
8068 o storing in gad_advection (plus removal of write(0,*)!
8069 o missing headers TR1.h added in convective_adjustment routines
8070 o errorMessageUnit set non-equal zero in eeboot
8071 (conflict on some platforms, e.g. IBM SP3)
8072 o modified carbon verif.
8073
8074 checkpoint44h_pre (2002/03/14)
8075 o vertical grid option: allow to put the Interface at the middle between
8076 2 cell-centers ; replace delZ in pkg/kpp by drF.
8077 o GM Advective form: Tracers are advected using the residual transport (=
8078 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
8079
8080 checkpoint44g_post (2002/03/05)
8081 o fix surface correction term in multiDimAdvection (affects plume_on_slope
8082 results) ; ifdef missing in thermodynamics.F
8083
8084 checkpoint44f_pre,checkpoint44f_post
8085 o added PTRACERS package
8086 This allows an arbitrary number of passive tracers to be integrated
8087 forward simultaneously with the dynamicaly model.
8088 + Implemented so far:
8089 - basic forward algorithm (time-stepping, advection, diffusion, convection)
8090 - I/O and checkpointing
8091 - GM/Redi *but* using the GM/Redi coefficient of Salt
8092 + Not implemented so far:
8093 - KPP
8094 - OBCS
8095 + No specific example supplied (yet) but global_ocean.90x40x15 has the
8096 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
8097 line in data.pkg.
8098 + This package is disabled by default since it increases storage.
8099
8100
8101 o testscript: added -cleanup option
8102 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
8103 b) enable to filter 2D fields.
8104
8105 checkpoint44e_pre,post
8106 o re-wrote convective adjustment to use pre-calculated weights
8107 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
8108 Adds: model/src/convective_weights.F, convectively_mixtracer.F
8109 Original calls to convect() still in place.
8110
8111 chkpt44d_pre,post
8112 o added missing EXCLUDE_MONITOR flags
8113 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
8114 (incompatible typ in MIN/MAX expressions caused problems
8115 on IBM SP3)
8116 o in genmake added variable MAKEDEPEND
8117 plus resetting for case SunOS
8118 o added timer_stats.c routine for IBM SP3
8119 o removed variables in dynamics
8120 !!! I forgot to create tag chkpt44d_pre !!!
8121 !!! But chkpt44d_pre = chkpt44c_post !!!
8122
8123 o real fresh water flux implemented with non-linear free-surface.
8124
8125 chkpt44c_pre,post
8126 o few fix (mask in shap_s2, EmPmR in external_field_load,
8127 USE_NATURAL_BCS in solve_for_P);
8128 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
8129
8130 checkpoint44b_pre/_post
8131 o merge of relevant stuff from the ecco-branch:
8132 - genmake: removed $S64 overwrite for case SunOS
8133 - pkg/exf: update and corrections for field swapping and obcs
8134 - pkg/ecco: parameter lists for the_model_main, the_main_loop
8135 harmonized between ECCO and MITgcm
8136 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
8137 updated checkpointing_lev... lists for obcs
8138 - model/src: minor changes in forward_step, plot_field
8139 added directive for divided adjoint in the_main_loop
8140 - pkg/mdsio: added mdsio_gl_slice
8141
8142 o check parameters & config (chkpt44a_pre,post)
8143 o OBC and NonLin_FrSurf.
8144
8145 checkpoint44 (2002/01/18)
8146 o fix bug in mom_vi_del2uv
8147 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
8148 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
8149 o update AIM experiments (NCEP input files)
8150 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
8151 o added some stuff for AD
8152
8153 checkpoint43 (2001/09/28)
8154 o added two new advection tests
8155 o added global 4x4 degree ocean test
8156 o added test of H&S94 with free surface on cube
8157 o some final mods for gradient check, adjoint,...
8158
8159 checkpoint42 (2001/09/27)
8160 Fixed AD-related problems:
8161 o Store directives up-to-date with re-arranged Adams-Bashforth
8162 (mainly thermodynamics.F)
8163 o New store directives for multi-dim. advection schemes
8164 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
8165 * new common block and key passkey
8166 (mainly gad_advection.F)
8167 o Modified store directives for split of dynamics/thermodynamics
8168 for the case ALLOW_KPP
8169 o Cleaned argument list for timestep_tracer.F
8170
8171 checkpoint41 (2001/09/27)
8172 o re-formatted/added comments in prologues of key subroutines
8173 to work with protex
8174
8175 checkpoint40 (2001/09/27)
8176 o moved calc_gs, calc_gt and calc_tr1 back to model/src
8177 o added FLT (floats) package from Arne along with demo. experiment
8178 o re-arranged Adams-Bashforth scheme for tracers to allow easier
8179 implementation of forward-in-time forcing terms
8180 o more mods for non-linear free-surface including new variable
8181 o modified multi-dim method to work on cube
8182 o bug fix in KPP (from DM)
8183
8184 checkpoint40pre9 (2001/09/27)
8185 o added DST advection schemes
8186 o fix MPI bug on SGI's
8187 o modifications for non-linear free-surface
8188 o fixed conditionals for fixed flow/passive tracer only mode
8189 o added tension/strain form of stress tensor
8190 o changes to commenting of arguments for TAF/TAMC
8191 o added/updated many matlab scripts
8192 o added multi-dimensional advection method for tracers
8193
8194 checkpoint40pre8 (2001/09/05)
8195 o new package rw/
8196 Added method for dumping intermediate local arrays:
8197 mdsio_writetile - same as mdsio_writefield except works from inside
8198 bi,bj loop
8199 mdsio_writelocal - same as mdsio_writetile except works for local
8200 arrays
8201 write_local_r? - higher-level wrapper for mdsio_writelocal
8202 Controlled by diagFreq. Defaults to zero (ie. no dumps)
8203 Example given at end of mom_vecinv.F that dumps some local arrays.
8204 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
8205 control flux-form versus vector invariant code.
8206 Switch is runtime flag vectorInvariantMomentum (defaults to false)
8207 or genmake -DISABLE ...
8208 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
8209 (additional storing is now needed for case vecinv;
8210 currently nothing implemented to switch this storing off
8211 in case fluxform is used since no CPP flag available).
8212
8213 checkpoint40pre7 (2001/08/14)
8214 o bug fix in dynamics.F
8215 calc_viscosity called before k=1,Nr loop.
8216 o added some #ifdef's ALLOW_PASSIVE_TRACER
8217 o cleaned initialisations in ctrl_map_ini
8218 related to TAF
8219
8220 checkpoint40pre6 (2001/08/13)
8221 o split dynamics into thermodynamics & dynamics
8222 o corresponding split of calc_diffusivity into
8223 calc_diffusivity, calc_viscosity
8224 (kpp_calc_diff, kpp_calc_visc).
8225 o Added diffkr, kapgm to control variables
8226 o bug fix in gmredi_slope_limit for ldd97
8227
8228 checkpoint40pre5 (2001/07/31)
8229 o proper initialization of Adams-Bashforth time stepping
8230 + uses forward step for very first step of model (iter=0)
8231 o re-generated *all* output since almost all output is modified by this
8232 change (sorry but we've been putting this one off for about 2 years)
8233 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
8234 *not* regenerated since they are already out of date and I don't
8235 want to create the impression that they are suddenly working.
8236 o removed KAP stuff for DEC's
8237 o modified/added many .cvsignore files in */code and */input
8238 o added new expt "solid-body.cs-32x32x1"
8239 + this uses an alternative form of ini_curvilinear_grid.F which
8240 is not necessarily any better than the current one...
8241
8242 checkpoint40pre4 (2001/07/30)
8243 o added re-initialisations of utrans,vtrans,rtrans in
8244 calc_common_factors which are crucial for TAF.
8245 o extended iMin,jMin range for calc_common_factors,
8246 calc_diffusivity
8247 o added option ALLOW_PASSIVE_TRACER
8248 o a few minor updates and fixes
8249
8250 checkpoint40pre3 (2001/07/13)
8251 o created calc_gtr1.F for gad package
8252 o split the_main_loop and re-introduced forward_step
8253 o some recomputations of nIter0 for TAMC
8254
8255 checkpoint40pre2 (2001/07/13)
8256 o Updated to latest branch of AJA, JMC
8257 o Added gradient check package
8258 o Added routines for passive tracer handling
8259 o Added carbon sequestration sensitivity experiment
8260
8261 checkpoint39 (2001/05/14)
8262 o Modifications and fixes to support TAMC
8263 (mainly missing or wrong directives)
8264 o Corrected common blocks when fooling TAMC to produce adjoint I/O
8265 in addummy_in_stepping
8266 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
8267 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
8268 o Included following packages:
8269 cal: calendar
8270 exf: external forcing
8271 ecco: essential routines to control use of cal, exf
8272 (NB: this is not the full ECCO environment)
8273 o disabled some packages by default in genmake
8274
8275 checkpoint38 (2001/04/10)
8276 o see notes_c37_adj.txt
8277 o corrected wrong layer index in external_forcing_t
8278 o replaced the_main_loop/forward_step by the_main_loop
8279 o removed forceoutput from write_state
8280 (replaced criteria for initial/final state)
8281 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
8282
8283 checkpoint37 (2001/03/13)
8284 o mdsio.F routine split and packaged in pkg/mdsio
8285 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
8286 used unless genmake -disable=mdsio)
8287 o allow a more precise surface-geopotential gradient for the atmosphere
8288 taking into account the change in space of Alpha (=1/rho) at the surface.
8289 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
8290 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
8291 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
8292 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
8293 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
8294 o Time-Average diagnostics defined as a pseudo package "timeave".
8295 o pickup files : old pickup (before c35) did not work with new code (c35
8296 and after) unless activating 2 commented lines in initialise-varia.
8297 o Non-Hydrostatic pickup file Pb fixed.
8298 o bug with Rigid-lid version (since c35) fixed.
8299
8300 checkpoint36 (2001/02/20)
8301 o implement Crank-Nickelson barotropic time-stepping
8302 o recover Time-Average diagnostics
8303 o fix Pb in checkpoint (PR#19)
8304 o AIM become a standard package ; clean unused CPP_kees
8305
8306 checkpoint35 (2001/02/08)
8307 o subtantial rewrite of dynamics.f
8308 o allows staggered time-stepping
8309 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
8310 o added bottom drag (linear + quadratic)
8311
8312 checkpoint34 (2001/01/30)
8313 o Modified exchange routines for correct reverse simulation.
8314 o Added verification output to comply with bug fix in impldiff.F
8315 as of c33 (exp2, natl_box).
8316 o Corrected store directives in dynamics.F
8317 o Corrected array boundaries in impldiff.F
8318 o Corrected array dimensions in gmredi.
8319 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
8320 o Added routine GLOBAL_SUM_INT to global_sum.F
8321 o Added mdsio_gl.F for ECCO purposes.
8322
8323 checkpoint33 (2000/11/30)
8324 o Fixed bug in lower BC in impldiff.F
8325 o Fixed confusion about units of forcing arrays in FFIELDS.h
8326 namely Fu,Fv,Qnet,Qsw,EmPmR:
8327 - Removed verification/natl_box/code/external_fields_scale.F
8328 (did not differ from that in model/src)
8329 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
8330 (see FFIELDS.h for description)
8331 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
8332 kpp_calc.F and kpp_transport_t.F
8333 - Removed model/src/external_fields_scale.F and calls to it
8334 - verification/natl_box uses flux data with "atmospheric" sign so
8335 a special version of external_fields_load.F is used to
8336 change the data as it's read in. This way, the arrays
8337 have the right units and signs at all times tha a user could
8338 possibly use them.
8339 o Corrected genmake to delete a temporary file during configuration
8340
8341 checkpoint32 (2000/11/13)
8342 o Scaling of forcing fields moved from external_forcing.F to
8343 external_fields_scale.F, called directly after loading fields.
8344 o Surface relaxation terms added to surface tendency fields in
8345 extra subroutine.
8346 o impldiff.F changed to avoid storing by TAMC of huge intermediate
8347 fields.
8348 o Changes in GMRedi to comply with packaging structure.
8349 o Modifications and bug fixes in KPP package.
8350 o Verification experiment for KPP added (verification/nat_box/)
8351
8352 checkpoint31 (2000/09/11)
8353 o Packages interface brought in line with defined standard
8354 -> new routines packages_...F
8355 -> changes in initialise_fixed.F, initialise_varia.F
8356 -> enables initialisation interface for ECCO package
8357 o Rescaling of external forcing fields immediately after read
8358 (removed from external_forcing.F)
8359 -> new: surface_fields_scale.F
8360 -> affects ini_foorcing.F, external_fields_load.F
8361 o Computation of surface tendencies before tendency updates.
8362 -> new: external_forcing_surf.F
8363 o Change of variable names useGMRedi, useKPP, useECCO
8364 o Further changes in dynamics.F, impldiff.F for TAMC
8365 o Tested for experiments 0, 2, 4.
8366 - not yet tested for GMRedi.
8367 - not yet tested for KPP.
8368
8369 checkpoint30 (2000/07/13)
8370 o Updates for OBCs
8371 o New experiment for test OBCs (internal_wave)
8372 o New output.txt in verification/exp4/results/
8373 o Updates for KPP: calculation of viscosity corrected, new variables
8374 kpp_dumpFreq and kpp_taveFreq
8375 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
8376 and entry for T90 in genmake
8377
8378 checkpoint29 (2000/06/21)
8379 o packaged KPP and GM/Redi
8380
8381 checkpoint28 (2000/06/09)
8382 o Corrected initialization of hFacMin for difference vertical coordinates
8383 o Modified calculation of partial cell thickness to more robust algorithm
8384 o config_summary.F: replaced write_1D_... by write_0D_...
8385 read_write.F: added subroutines write_0D_...
8386 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
8387 included some initialisations required for TAMC.
8388 o routine calc_isoslopes: modified sqrt computation to make it
8389 differentiable for zero argument.
8390 o routines dynamics, impldiff:
8391 included store directives and tape key computations required for TAMC.
8392 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
8393
8394 checkpoint27 (2000/04/10)
8395 o fixed calc_isoslopes() to so that cancellation of terms in tensor
8396 formulation works properly with variable resolution.
8397 o restructured the calling tree between the_model_main() and dynamics()
8398 o split initialise() into initialise_fixed() and initialise_varia()
8399 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
8400 in new routine ini_psurf()
8401
8402 checkpoint26 (2000/04/05)
8403 o moved some #ifdef in optional routines to encompass everything
8404 except the argument declarations. This was using up some memory.
8405 o fixed macros like _ADT to work with both versions of Linux cpp
8406 o cleaned up some unused and uninitialized variables
8407 (helps when debugging with strict compile options)
8408 o split up CPP_EEOPTIONS.h into options and macros
8409 (macros are now in eesupp/inc/CPP_EEMACROS.h)
8410 o patch for 2 processor JAM mode
8411
8412 checkpoint25 (2000/03/15)
8413 o updates for OBCs and NH
8414 o dramatically reduced memory usage
8415 o added "JAM" routines for use on Artic network
8416 o parameterization of convection by implicit vertical diffusion
8417 o added a diagnostic of convective index
8418 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
8419 (this is was partly for OBCs and NH but also in anticipation of
8420 an explicit free-surface option)
8421 o initial state input files for U and V
8422
8423 checkpoint24 (1999/08/02)
8424 o Removed some spurious "REAL"s
8425 o Updated KPP to latest version from JPL
8426 o Added a COS(latitude) in horizontal viscosity
8427
8428 checkpoint23 (1999/05/26)
8429 o Added del^4 diffusion for salt and temperature
8430 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
8431
8432 checkpoint22 (1999/05/18)
8433 o Made many small changes: implicit none, format(i5), etc...
8434 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
8435
8436 checkpoint21 (1999/05/18)
8437 o Introduced new I/O package that supports direct-access records (mdsio.F)
8438 o Split-up mid-level I/O routines
8439 o Updated input data for experiments 0,1,2,4 and 5
8440 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
8441
8442 checkpoint20 (1999/03/22)
8443 o Tidied up open-boundaries some more
8444 o Added non-hydrostatic code
8445 o Fixed some input data
8446 o Modified MPI start-up to work in "coupled" context.
8447
8448 checkpoint19 (1998/12/15)
8449 o Tidied up directory structure for verification experiments.
8450 o Added new code for open boundaries.
8451 o Corrected advective terms near boundaries.
8452 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
8453 o Implemented free-slip/no-slip BCs and del^4 dissipation.
8454 o Split default parameters out of ini_parms.F into set_defaults.F.
8455
8456 checkpoint18 (1998/11/30)
8457 o Further changes for optional code generation with
8458 CPP - ugh!
8459
8460 checkpoint17 (1998/11/03)
8461 o Beginning to incorporating modularity
8462 for supporting atmos. and ocean configs.
8463 o Small changes for TAMC complinace
8464 o New ultra simple test case. Barotropic box
8465 configuration "exp0".
8466
8467 checkpoint16 (1998/10/28)
8468 o Minor changes to exchange routines to support
8469 accumulation in reverse mode. Adjoint of an
8470 assignment is an addition.
8471 o Changes to support compilation by TAMC (LR(1)
8472 syntax) and by g77 under Linux ( 72 character
8473 limit ).
8474
8475 checkpoint15 (1998/09/29)
8476 Rewrote exchange routines to allow
8477 o General tile <-> tile connectivity.
8478 o TAMC reverse mode flag ( is this really needed? )
8479 o Variable width overlap and exchange region widths.
8480 o Hooks for sharing data via DMA, Arctic, Memory Channel,
8481 shmput/shmget, VIA, SYSV shmem and every other cool
8482 communication method.
8483
8484 checkpoint14 (1998/09/09)
8485 Consistent isomorphism chages made. These allow dynamical core
8486 to support both pressure and meters as a vertical coordinate.
8487
8488 checkpoint13 (1998/07/17)
8489 Release which corrects global_max problem and a couple
8490 of KGM time-averaging diagnostic errors. Also contains
8491 a double-gyre experiment setup as well as the baseline
8492 4 degree global template. The double gyre template is
8493 organised to allow it to be applied automatically to
8494 the baseline configuration.
8495
8496 branch-point-rdot
8497 A few tidy-ups have been made bt the real point of this
8498 check-point (excuse the pun) is to allow a branch to be
8499 made for the purposes of adding the rDot alterations.
8500 I don't want to commit the rDot to the main-trunk until
8501 we've actually tested it...
8502
8503 checkpoint12 (1998/07/08)
8504 Tidy up and added generic genmake script (formerly
8505 configure script).
8506 Released to testers.
8507
8508 checkpoint11 (1998/07/02)
8509 Re-arranged initialise() and introduced ini_vertical_grid()
8510 and ini_masks_etc().
8511
8512 checkpoint10 (1998/07/01)
8513 Introduced the configure script.
8514 Separated out the diags package.
8515 Added template for writing time-averages of tile/intermediate quantities.
8516 Updated SIZE.h in exp2 and made the data big-endian.
8517
8518 checkpoint9 (1998/06/22)
8519 MPI fix. Filename changes (meta/data). salbin*y stuff.
8520 General tidy-up.
8521 SST.bin SSS.bin added to verification/exp2
8522
8523 checkpoint8 (1998/06/22)
8524 Inludes time-dependant forcing and time-averaging.
8525 Works at 4x4 and 2.8125x2.8125 global
8526
8527 checkpoint7-4degree-ref
8528 Branch from checkpoint7. Released for application to
8529 global modeling and general modeling - process studies, regional
8530 model etc..
8531 Configured for verification/exp2 - 4 degree global, two process.
8532
8533 checkpoint7 (1998/06/15)
8534 Created by cnh
8535 Simple 4 degree global simulation
8536 configuration.
8537 Includes climatological wind,
8538 hydrography, bathymetry etc
8539 Does not include Heat Flux and E-P
8540
8541 checkpoint6 (1998/06/08)
8542 Created by cnh
8543 merged checkpoint5 with CD and
8544 spherical polar code.
8545 Still some problems with GM Redi
8546 abd full topography.
8547
8548 checkpoint5 (1998/06/08)
8549 Created by AJA
8550 contains updates to GM Redi
8551 and reordered timestepping loop
8552 for Implicit Diffusion.
8553
8554 checkpoint4 (1998/05/30)
8555 Created by cnh
8556 Contains memory saving macros ( _rdxc etc..) for when
8557 grid variations are limited.
8558 Contains polynomial coeffs for EOS and knudsen program
8559 for generation.
8560
8561 checkpoint3 (1998/05/26)
8562 Created by cnh
8563 Added extra flags for runtime options
8564 Added this file
8565 Added implicit free-surface
8566 Added pre-conditioner
8567 Put compare01 into repository ( compare01/... )
8568 Put data and eedata into repository ( verification/exp1 )
8569
8570 checkpoint2
8571 Created by AJA
8572 Added GM/Redi
8573
8574 checkpoint1
8575 Created by AJA
8576 Restructured kloop in dynamics.F
8577 Added non-linear EOS
8578
8579 baseline
8580 Original checked in code

  ViewVC Help
Powered by ViewVC 1.1.22