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Revision 1.1271 - (hide annotations) (download)
Mon May 17 14:23:42 2010 UTC (14 years ago) by mlosch
Branch: MAIN
Changes since 1.1270: +3 -1 lines
document rewriting of exf_bulk_largeyeager04.F for better
vectorization, changes global_ocean.cs32x15/input.icedyn (11 digits of
agreement), updated

1 mlosch 1.1271 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1270 2010/05/17 02:32:49 jmc Exp $
2 jmc 1.475 $Name: $
3 cnh 1.1
4     Notes on tags used in MITgcmUV
5     ==============================
6 dfer 1.1157
7 mlosch 1.1271 o pkg/exf/exf_bulk_largeyeager04.F: rewrite for better vectorization, changes
8     global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
9 jmc 1.1270 o eesupp/src (exch-1):
10     - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
11     - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
12     array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
13     (even without using MPI).
14     - Message mode: move RecvAck setting (indicator of buffer being ready)
15     from send_put to recv_get S/R (was useless before, but not sure if
16     it's much more useful now);
17     - switch the order of sync: MPI-proc 1rst and then threads;
18     - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
19 jmc 1.1269 o model/src:
20     initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
21     not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
22 mlosch 1.1268 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
23 mlosch 1.1267 o pkg/ctrl: require a specific set of control variables and exf-flags for
24     adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
25 gforget 1.1264 o model/src:
26 jmc 1.1266 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
27     1rst forward sweep, to avoid over-writing output files during recomputations
28     recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
29     b) 2nd version:
30     - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
31     - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
32     writePickupAtEnd) + seaice & ptracers output;
33     - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
34 jmc 1.1265 o model/src:
35 gforget 1.1264 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
36 jmc 1.1263 o pkg/exch2:
37 jmc 1.1265 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
38 jmc 1.1263 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
39 jmc 1.1262 o pkg/autodiff & exch2:
40     process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
41     (for now, only if ALLOW_EXCH2 is defined).
42 jmc 1.1261 o pkg/autodiff:
43 jmc 1.1265 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
44 jmc 1.1261 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
45     + clean-up comments (_RS is not always real*4)
46     - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
47     - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
48     was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
49 jmc 1.1260 o testreport (AD-tests):
50     no longer link files from dir "../input" (1rst link files from
51     "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
52    
53 jmc 1.1259 checkpoint62f (2010/04/29)
54 mlosch 1.1258 o model/src/the_main_loop.F:
55     adjust store directives for seaice evp and multicategory according to
56     pkg/ecco/the_main_loop.F
57 heimbach 1.1256 o adjoint:
58 jmc 1.1260 global_sum_ad was incomplete (noted many times by many people ;)
59 heimbach 1.1256 nice description by Jean U. as follows:
60 jmc 1.1260 * allreduce(var) in global_sum.F can be interpreted as
61     reduce(sum) followed by broadcast of sum.
62     * The adjoint of that is
63     sum(adjoint) followed by broadcast(summed adjoint value)
64 heimbach 1.1256 or in other words, allreduce(sum, adjoint vars)
65     We were missing the sum(adjoint)!
66     Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
67     (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
68     The fix should produce 16-digit accuracy between
69     single-CPU multi-tile (e.g. nSx=2, nPx=1) and
70     multi-CPU single-tile (e.g. nSx=1, nPx-2)
71     We'll probably change this yet again shortly
72 jmc 1.1257 o eesupp/src:
73     - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
74 dimitri 1.1255 o pkg/icefront
75     - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
76     specification of addmass array based on a 2D field, which is added
77     at bottommost wet level at each horizontal location.
78 jmc 1.1254 o model/src:
79     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
80     layout; (not always compatible with delX,delY setting; commented out for now).
81 jmc 1.1253 o pkg/exch2:
82     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
83     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
84    
85 jmc 1.1252 checkpoint62e (2010/04/15)
86 jmc 1.1251 o pkg/obcs:
87     - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
88 jmc 1.1250 o pkg/dic:
89     -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
90     (note: not presently tested in any forward verification exp.)
91     update tutorial_global_oce_biogeo AD output file.
92     o pkg/exf:
93 gforget 1.1249 - account for the variation of albedo as a function of zenith angle
94 jmc 1.1250 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
95 jmc 1.1248 o build_options:
96     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
97     o pkg/dic:
98     change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
99     - use binary pickup file for restart;
100     - initialise atmos-CO2 box from dic_pCO2 parameter;
101     - fix multi-threaded.
102 jmc 1.1247 o pkg/rbcs:
103     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
104     change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
105     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
106     and update output.txt
107 jmc 1.1246 o pkg/kpp:
108     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
109     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
110 jmc 1.1248 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
111 jmc 1.1246 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
112     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
113     KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
114 dfer 1.1244 o pkg/offline:
115 jmc 1.1245 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
116     (bug was added in version 1.10 on 2007-08-23).
117     o pkg/offline:
118 dfer 1.1244 - no need to specify periodicExternalForcing, etc ... to use offline pack
119     - offline input files no longer just single prec --> parameter offlineLoadPrec
120 heimbach 1.1242 o verification/lab_sea:
121 jmc 1.1245 change AD test to multi-tile setup and update all 4 AD output.
122 heimbach 1.1242 NOTE: while cost function values remain very similar,
123     gradients are very different, although gradient checks are self-consistent
124     Should try to get to the bottom of this (cost function summation order?)
125 jmc 1.1241 o pkg/dic:
126     in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
127     a weakness of TAF that drops part of double precision in log10 derivative.
128 jmc 1.1243 <= changes removed since problem has been fixed in current TAF version 1.9.71
129 jmc 1.1241 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
130 jmc 1.1240 o pkg/ecco:
131     add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
132     update all 4 lab_sea AD output.
133    
134 jmc 1.1239 checkpoint62d (2010/03/22)
135     o build_options:
136     remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
137 jmc 1.1238 o remove unbalanced quote (single or double) in commented line of source code
138     (may cause some warning with some preprocessor/makedepend versions).
139     o pkg/seaice:
140 jmc 1.1237 fix seaice_model.F for adjoint (gael) and update AD results of experiments
141     lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
142 jmc 1.1236 o testreport:
143     add option '-runonly' (short: '-ro') to just do the run part (without make).
144 jmc 1.1235 o eesupp: remove JAM communication code (obsolete).
145 jmc 1.1234 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
146     (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
147     to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
148     (update also the output).
149    
150 jmc 1.1233 checkpoint62c (2010/03/02)
151 jmc 1.1232 o tools/build_options :
152     move (some) old optfiles from build_options/ to build_options/unsupported/
153 gforget 1.1231 o model/src and pkg/exf
154     surface relaxation -- separating data and data.exf options
155     The point is to ensure that we specify the surface relaxation
156     either in data or in data.exf (but not half and half) and to
157     avoid an accidental relaxation to 0 (which happened if a time
158     scale was specified but the file name was left empty)
159 gforget 1.1230 o model/src model/inc and pkg/mom_common
160     ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
161     => addition to the viscosity field as computed by others schemes
162 jmc 1.1229 o tools/build_options:
163     - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
164     but keep the former optfile for few weeks for smooth transition
165 gforget 1.1228 o pkg/ecco
166     - allow user defined cost function contributions
167     CPP: ALLOW_USERCOST_CONTRIBUTION
168     USAGE: compute contributions in cost_usercost_all.F
169     - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
170     the two options are complementary.
171 gforget 1.1227 o pkg/smooth
172     - migration from contrib to the main repository
173 jmc 1.1229
174 jmc 1.1226 checkpoint62b (2010/01/26)
175 jmc 1.1225 o pkg/monitor:
176     - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
177     (in case someone forgot to update customized pieces of code)
178     o nonHydrostatic:
179 jmc 1.1224 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
180     - add a simple 2-D experiment (short_surf_wave) to test it.
181     o pkg/icefront:
182     adding the shell of, and the hooks to, a new package that
183 dimitri 1.1223 will model melting and freezing of vertical glacier ice fronts
184 jmc 1.1224 o momentum:
185 jmc 1.1222 add diagnostics of momentum tendency from Hydrostatic pressure gradient
186     (without surf.pressure term: would need a 2nd filling since implicit term).
187 jmc 1.1224 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
188     two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
189     cannot deal with the former
190 jmc 1.1220 o cleaning:
191 jmc 1.1222 - remove all (except OpenAD) old TLM output from results_ad dirs.
192 jmc 1.1220 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
193     - comment out maskH definition (replaced by maskInC)
194     o pkg/monitor:
195     - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
196 jmc 1.1225 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
197 jmc 1.1220
198 jmc 1.1219 checkpoint62a (2010/01/15)
199 jmc 1.1218 o model/src:
200     - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
201 jmc 1.1217 o pkg/diagnostics:
202     - add optional level number diagnostics (i.e., level number to be define
203     explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
204     - strictly check for valid parser-code(10) ;
205     - check if adding diag to the list from the right place.
206 jahn 1.1216 o pkg/longstep:
207     - change parameters and fix tracer conservation with rstar/nonlinear free surface
208 jmc 1.1215 o diagnostics:
209     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
210     S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
211 jmc 1.1214 o pkg/diagnostics:
212     - Add option for writing vertical integral (sum of selected levels) of an output
213     field instead of writing output field levels. Activate this option on a per
214     output-file basis, by setting the 2nd character of fileflag to 'I'.
215     - Add field-specific information relative to level integral in 3rd postion
216     of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
217     vertically (x level-thickness x hFac), "r"=same but without hFac.
218 jmc 1.1213 o do_the_model_io:
219     - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
220     in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
221     writing pickups and stopping.
222     o pkg/diagnostics (for now, only with mdsio):
223     - write time information to meta file (and modify accordingly rdmds.m) :
224     time-averaged diagnostics output: write starting and ending time of the
225     time-averaging interval ; snap-shot diagnostics output remains unchanged;
226 jmc 1.1212 o pkg/timeave:
227     - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
228     always Nr), now assumed to be equal to number of levels of averaged field;
229     only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
230     o pkg/sbo:
231     - fix ocean bottom pressure global-average & 2-D time-ave output (was
232     neither initialised nor filled).
233     - add starting iteration in suffix of global-average output file
234     (to avoid over-writing the file after a restart)
235     - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
236     o time-average:
237     - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
238     (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
239     ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
240     this fix DIC_COST cumulative-time array (previously: bi,bj,k)
241     - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
242     - fix missing accumulation for pkg/opps.
243     - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
244     (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
245     - fix initialisation of time-ave vars and do only full time-step increment
246     (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
247 jmc 1.1211 o pkg/layers:
248     - use standard RW pkg S/R to write the output
249     and remove local write_fld version (which had a problem).
250     - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
251     - fix LAYERS_CALC argument list.
252     o pkg/timeave:
253     - store cumulative-time in a simple tiled array (drop the level index)
254     - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
255 jmc 1.1210 o pkg/ocn,aim_compon_interf
256     - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
257    
258 jmc 1.1209 checkpoint62 (2009/12/23)
259 jmc 1.1208 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
260     (was not previously tested in any other exp.)
261 jmc 1.1207 o pkg/monitor:
262     - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
263 jmc 1.1209 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
264 jmc 1.1207 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
265     - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
266     - change del2 calculation.
267     - use interior masks (instead of maskH, <- to be remove).
268     - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
269     o mask & obcs:
270     - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
271 jmc 1.1209 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
272 jmc 1.1207 (called after packages_init_fixed)
273 jahn 1.1206 o pkg/obcs:
274     - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
275     Fixes bug in obcs+exf with nSx*nSy.GT.1
276     - fix multi-tile handling in obcs balance code
277 jmc 1.1205 o nonHydrostatic:
278     - Implement AB-3 for non-hydrostatic vertical momentum ;
279     (change ordering of var. stored in pickup file when using NH)
280     - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
281     - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
282     (in prep. for new NH free surface form).
283 jmc 1.1204 o pkg/obcs:
284     add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
285 jmc 1.1209 o model/src:
286 jmc 1.1204 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
287    
288 jmc 1.1203 checkpoint61z (2009/12/01)
289 jmc 1.1202 o nonHydrostatic:
290     Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
291     a spurious source of energy in simple baroclinic adjusment test case.
292     Update all non-hydrostatic exp output.
293     o model/src (3-d solver):
294     Change again 3-D solver free-surface RHS term when exactConserv=T:
295     simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
296     (which was not the case with previous formulation).
297     To recover previous version, just reset "oldFreeSurfTerm" to previous value.
298     Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
299     o nonHydrostatic:
300     - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
301     for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
302     - change 3-D solver to work with r* (for now, only with linear free-surf.)
303     - add few debug diagnostics (cg3d_x, residual)
304 jmc 1.1201 o model/src:
305     fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
306     update output of exp. global_ocean.cs32x15.viscA4
307 jmc 1.1200 o update output of exp. global_ocean.cs32x15.icedyn after removing
308     #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
309     o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
310 mlosch 1.1199 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
311     for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
312 mlosch 1.1198 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
313 jmc 1.1200 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
314     runtime flag useSRCGSolver. Modify verification experiment global_with_exf
315     to test this code
316 jmc 1.1197 o pkg/cd_code:
317     Change defaut D-grid time-stepping to get the same for D-grid momentum as for
318     C-grid momentum. D-grid velocity used to be stepped forward in time with
319     Adams-Bashforth only on surface pressure term. Tests show that using AB on
320     D-grid coriolis term improves stability (as expected from CD-scheme paper).
321     To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
322     Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
323     lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
324     tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
325     Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
326 jmc 1.1204 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
327 jmc 1.1196 o pkg/obcs:
328 jmc 1.1197 - fix bug in initialisation (broken since Oct 1rst modification)
329 jmc 1.1196 for useOBCSprescribe without useEXF.
330    
331 jmc 1.1203 checkpoint61y (2009/11/15)
332 mlosch 1.1194 o pkg/seaice
333     - change (once again) the discretization for the evp solver: rather than
334     squaring the averages of strain rates, average the squares to give
335     a better approximation to VP behavior (in simple test); this breaks
336     verification experiments that use EVP (lab_sea and lab_sea.hb87)
337     --> update outputs
338 jmc 1.1195 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
339 mlosch 1.1193 to improve vectorization of adjoint code on TARGET_NEC_SX
340 dfer 1.1192 o verification/vermix:
341 mlosch 1.1194 - change vermix to a more "classical" 1d column with high vertical
342     resolution, seasonal heat flux forcing and constant wind forcing
343     --> update outputs
344 mlosch 1.1190 o pkg/seaice
345     - fix diagnostics of principal stress components for EVP
346     - add optional diagnostics of non-linear convergence for LSOR solver
347 mlosch 1.1191 - make maximum zeta a runtime parameter
348 jmc 1.1189 o model/src (3-d solver):
349     Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
350     which consisted in removing the Surf. Non-Hydrostatic pressure from the
351     whole column and adding it to Eta (inspired from Casualli, 1999):
352     Only affects 3-D solver initial guess and only if using ExactConserv,
353     but tests did show a degradation of solver convergence. For this reason,
354     decide to disable this piece of code.
355     to recover previous version, just set zeroPsNH = exactConserv (line 78).
356     Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
357 jmc 1.1188 o pkg/ggl90:
358     - fix previous modif (unfortunatly has not been documented here).
359 mlosch 1.1182 o pkg/seaice/autodiff:
360 mlosch 1.1185 - add CPP flag to include clipping of zeta in EVP code;
361     although clipping of zeta is not necessary for EVP and not recommended
362     it was done by default, now clipping is disabled by default
363 mlosch 1.1184 - modify computation and store zetaC/Z in seaice_evp for TAF
364 mlosch 1.1183 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
365 mlosch 1.1190 - change seaice_calc_viscosities/strainrates for better
366 mlosch 1.1183 vectorization after AD by TAF
367 jmc 1.1187 - rearrange common blocks in SEAICE.h once again for easier dumps of
368 mlosch 1.1182 adjoint output, adjust adcommon.h and g_common.h
369     - change flux form of default advection scheme for better vectorization
370     of adjoint code
371     - modify lab_sea/input.lsr to test the flux form of default advection
372     scheme
373 mlosch 1.1181 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
374     transition in checkpoint61r)
375    
376 jmc 1.1203 checkpoint61x (2009/10/19)
377 heimbach 1.1179 o adjoint: adding two new verification experiments
378     * tutorial_global_biogeo: an online dic sensitivity experiment
379     (work with G. Forget)
380     * tutorial_dic_adjoffline: an offline dic sensitivity experiment
381     (an update of the Dutkiewicz et al., 2006 paper)
382     Both use the same CO2FLUX cost function, but different controls
383     Gradient checks look good, but some recomp. could still be traightened out
384     Should add xx_dic control variable to test at some point
385 jmc 1.1178 o model/src:
386     add run-time parameters to check and/or mask initial Temp & Salt
387 jmc 1.1177 o pkg/ptracers:
388     apply zonal filter (if used) to all passive tracers
389    
390 jmc 1.1203 checkpoint61w (2009/10/12)
391 heimbach 1.1175 o adjoint:
392     * update and finish work on adjoint of dic package (G. Forget)
393     * start adjoint of offline package
394     * bug fix for cube-sphere TLM code (active_file_g.F)
395 jmc 1.1173 o tutorial_global_oce_optim:
396     now tested with 4 tiles (change data.grdchk and update output_adm.txt)
397 jmc 1.1174 and add SIZE.h_mpi for MPI testing
398 mlosch 1.1172 o pkg autodiff
399     - fix bug in autodiff_restore
400     - make genmake2 remove comments and empty lines from ad_input_code.f in
401     order to reduce file size (new script file remove_comments_sed)
402 jmc 1.1171 o allows to specify vertical profile of vertical viscosity (viscArNr)
403 mlosch 1.1170 o pkg autodiff
404     autodiff_ini_model_io: comment out writing of grid information to netcdf
405     files, because at this time the grid fields are a bunch of zeros
406     (this is analogous to ini_mnc_vars.F)
407 mlosch 1.1169 o pkg seaice/autodiff:
408     left-over from removing the 3-time-level fields:
409     - small rearrangement of common blocks (SEAICE.h)
410     - fix field declaration in order to get meaningful output in
411     adseaice.*.nc (adcommon.h)
412 jmc 1.1165 o pkg obcs:
413     - go through NH code only if nonHydrostatic=T
414     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
415 jmc 1.1174 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
416 jmc 1.1166 => Update output of experiment seaice_obcs
417     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
418 jmc 1.1167 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
419 jmc 1.1168 - fix restart for useOBCSprescribe + useEXF
420 mlosch 1.1164 o pkg ctrl
421     - make obcs as control parameter work also with useSingleCPUio
422     - replace a few sny and snx by Ny and Nx to be consistent with
423     ctrl_set_globfld_x/yz.F
424 mlosch 1.1163 o pkg seaice
425     - re-introduce global field frWtrAtm for the case of
426     ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
427     - catch the case of an empty filename in seaice_cost_init_fixed.F
428     o pkg ecco:
429     - small bug fixes in the_main_loop
430     . fix order of monitor arguments
431     . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
432     . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
433     that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
434     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
435     imbalance diagnostics for wmean_h/sflux = 0
436     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
437     - catch the case of empty filenames in ecco_cost_init_fixed.F
438     and ecco_readparms.F
439     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
440 mlosch 1.1164 to make this statement meaningfull in ecco_cost_weights.F
441 jmc 1.1162 o pkg zonal_filt:
442     - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
443     - when using rStar, filter uVel*hFacW instead of uVel
444     (tested without topography: fix a Pb of growing instability with NLFS)
445 dfer 1.1161 o pkg/aim/thsice:
446     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
447     (works as SST restoring)
448 dfer 1.1160 o pkg/thsice:
449     -add specific parameter for salt restoring in slab mixed-layer
450     (by default equal to the temperature restoring)
451    
452 jmc 1.1203 checkpoint61v (2009/09/21)
453 mlosch 1.1158 o pkg/kpp:
454     -add double diffusive contributions as a hack, turned off by default
455     for now, and the code can be excluded with a CPP-flag
456     EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
457     -add a verification experiments to "vermix" to test this code
458 dfer 1.1157 o pkg/mom_common:
459     Move computation of length scales to mom_init_fixed.F (avoid recomputation
460     at each time-steps*levels).
461 rpa 1.1156 o pkg/layers:
462     Created a new package for computing volume fluxes in temperature or
463     [not yet implemented] density layers, e.g. for calculating residual
464     overturning circulations.
465 jmc 1.1155 o pkg/diagnostics:
466     implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
467     o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
468 jmc 1.1154 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
469     To avoid mixing type (RS/RL) of input/output array argument,
470     replace single mixed-type array with a pair from each type (RS/RL).
471 jmc 1.1153 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
472     is now implemented for all pkgs (previously only done for the main pickup)
473    
474 jmc 1.1203 checkpoint61u (2009/08/25)
475 mlosch 1.1150 o pkg/obcs:
476 mlosch 1.1151 - change OB?eta from _RS to _RL and put them into a separate commen block
477     - add code to read OB?eta from a file via obcs_prescribe_read: the code
478     compiles and does not destroy any other experiments, the data is read
479     properly, but the code is not tested in actual applications
480 mlosch 1.1149 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
481     create a meaningful unit attribute for the time coordinate variable
482 jmc 1.1148 o pkg/ebm: add plenty of missing "_d 0" ;
483     update results of experiment global_ocean_ebm (fwd + adjoint tests)
484     Notes: several pieces of code only works for (very) specific set up
485     (domain size, lat range, etc ...); should be documented & stop if one
486     of those assumptions is not meet.
487 jmc 1.1147 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
488     update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
489     and offline_exf_seaice (seaicetd + adjoint).
490 jmc 1.1146 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
491     update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
492     seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
493     o few changes to pass when compiling with strick checking of arguments
494     across S/R (allow to find few bugs in S/R calls).
495 mlosch 1.1145 o pkg/seaice:
496     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
497     2d-fields, for slightly better performance
498 jmc 1.1146
499 jmc 1.1203 checkpoint61t (2009/07/22)
500 mlosch 1.1142 o pkg/seaice:
501     - remove unused variables in seaice_evp
502     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
503 jmc 1.1141 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
504     named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
505 jmc 1.1144 each processor opens a different file (a fix from Matt).
506 jmc 1.1140 o cg2d:
507     use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
508     this reduces number of EXCH calls by 2 when using exch2.
509     For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
510     directives and missing simple EXCH (exch_s3d_rx) adjoint code.
511     o pkg/thsice:
512     add code for Near Infra-Red albedo (from Jeff)
513 jmc 1.1139 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
514 jmc 1.1140 o ini_model_io:
515     move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
516     MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
517     to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
518 jmc 1.1139
519 jmc 1.1203 checkpoint61s (2009/06/30)
520 jmc 1.1137 o pkg/exch2 (exch2_rxN_cube*):
521     remove last BARRIER (no need to synchronise after getting data from shared
522     buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
523 jmc 1.1136 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
524     and generate new output (for the 2 tests) using default rotationPeriod.
525 jmc 1.1135 o pkg/exch2:
526     - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
527     (was already the case with AUTODIFF_EXCH2 defined)
528     - add bj in exch2 arrays and S/R.
529 jmc 1.1136 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
530     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
531 jahn 1.1134 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
532     - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
533     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
534     - verification experiment natl_box.longstep
535 jmc 1.1133 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
536     allow different versions of ifort (8 or 9) and different versions
537     of mpi (mpich or mpich2) to be used with the same optfile.
538     requires to load a netcdf module and set MPI_INC_DIR (see comments inside
539     optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
540 jmc 1.1135 o pkg/seaice:
541     fix previous modif (3-level field removed) for old-pickup reading
542 jmc 1.1133
543 jmc 1.1203 checkpoint61r (2009/06/25)
544 mlosch 1.1129 o pkg/seaice:
545 mlosch 1.1130 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
546     1. introduce fields for time step (N-1)
547     2. do not use levels 2 and 3 anymore (but keep them)
548     3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
549     includes changes to pkg/thsice/thsice_get_velocity.F,
550     model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
551     pkg/obcs/obcs_apply_uvice.F.
552     - completely remove code for leap-frog time stepping for second order
553 mlosch 1.1129 advection
554 heimbach 1.1131 - adjusted adjoint accordingly;
555     gradient checks have improved by an order of magnitude!
556 mlosch 1.1130
557 jmc 1.1203 checkpoint61q (2009/06/22)
558 mlosch 1.1128 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
559     - the boundary conditions along open boundaries are unclear, because the
560     associated masks are set to zero and are thus treated as closed when
561     applying the slip-boundary conditions.
562     - move initialisation of grid variables from seaice_init_varia to _fixed
563 dimitri 1.1127 o adding doc/diags_changes.txt
564 jmc 1.1126 o model/src:
565     do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
566     to avoid "_diags" naming if no relation to pkg/diagnostics.
567     ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
568     file and only call PLOT_FIELD_XYZ if debugMode=T.
569     remove few PLOT_FIELD_XY calls outside initialisation.
570     remove few unnecessary BARRIER.
571 dimitri 1.1125 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
572     of salt_plume package in Southern Ocean
573 jmc 1.1124 o pkg/thsice:
574     - fix hOceMxL in overlap (needed for sea-ice advection);
575     update output of experiment global_ocean.cs32x15.icedyn.
576 mlosch 1.1123 o pkg/seaice:
577     - make the (placeholder-)tracer IceAge a little more meaningful
578 mlosch 1.1122 by avoiding ridging of age due to convergent ice flow
579 dimitri 1.1127 - add diagnostics for surface temperature, atmospheric and oceanic
580     heat flux, and atmospheric and oceanic ice growth
581 mlosch 1.1122
582 jmc 1.1203 checkpoint61p (2009/06/10)
583 jmc 1.1120 o eesupp (global_max & global_sum):
584     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
585     - remove starting & endding barrier (no longer needed)
586 jmc 1.1119 o pkg/mdsio, writelocal:
587     works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
588     (remove the STOP): uses shared buffer IO to store data from all threads
589     and then let master-thread write nThreads tiles.
590 jmc 1.1118 o pkg/mdsio (read/write field):
591     - tiled IO done in 1 piece (all levels at a time);
592 jmc 1.1119 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
593 jmc 1.1118 - multi-threaded: allow to read/write local (non-shared) array
594     (was already working with singleCpuIO ; now works also without);
595     => no longer needs barrier call after reading a file (added inside
596 jmc 1.1119 mds_read/write field).
597 jmc 1.1118 - move barrier calls outside gather/scatter_2d to mds_read/write_field
598 mlosch 1.1115 o pkg/obcs/exf
599 mlosch 1.1116 - exf_getffieldrec.F: add a few ". _d 0" and
600     add code to catch the case fldperiod = 0.
601 mlosch 1.1115 - obcs_precribe_read.F: change if statements so that they match
602     the variable type (_RL)
603     - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
604     exf_iprec) as part of namelist EXF_NML_01
605 jmc 1.1114 o pkg/mdsio:
606     - read/write tiled (local) files: read/write 1-level tile chunk at a time
607     (instead of segment of length sNx); expected to speed up tiled IO.
608     o pkg/exch2:
609 jmc 1.1113 - take buffer copy from/to array out of S/R exch2_send/recv into new
610     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
611     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
612     - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
613 jmc 1.1114 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
614 jmc 1.1113 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
615     including Topology header file (and common blocks).
616     - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
617     remove 2nd exch call in exch2_s3d_rx (no longer needed).
618     - document S/R arg. list (+ update some comments)
619 dimitri 1.1117 o pkg/seaice:
620     - added SEAICE_CLIM_AIR code, which permits modulation of surface air
621     temperature and humidity over sea ice based on climatological values.
622 mlosch 1.1111 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
623     of LSR (this change is expected to change the results slightly because now
624     it uses slightly difference moduli from the second last LSR solution, but
625     that is more consistent with the stress computations; this part of the code
626     is not tested in the verification experiments)
627 mlosch 1.1110 - fix diagnostics for flux of ice in case of B-grid
628     - turn strain rates eij and press into global fields within global
629     common block in SEAICE.h for more straighforward diagnostics
630     - fix diagnostics for principal stress components, press, zeta, eta
631     to give something meaning full
632 jmc 1.1109 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
633     new output (all 4 tests) using default rotationPeriod.
634 dfer 1.1112 o pkg KPP:
635     - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
636     - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
637     and normal grid from 1 to Nr)
638 dfer 1.1108 o Fix computations of L4rdt in mom_calc_visc.F
639 jmc 1.1107 o eesupp:
640     new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
641     should be called before a "stop" if we know that all process are going
642     to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
643    
644 jmc 1.1203 checkpoint61o (2009/05/26)
645 jmc 1.1106 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
646     o model/src/ini_curvilinear_grid.F:
647 mlosch 1.1104 compute angleSin/CosC when they are not read from a file
648 jmc 1.1106 o pkg/seaice:
649 mlosch 1.1104 add pseudo time stepping for LSOR
650 jmc 1.1103 o pkg/exch2:
651     temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
652 dimitri 1.1102 o pkg/seaice:
653 dimitri 1.1105 Adding separate sea ice albedo, drag coefficients, and HO in Southern
654     Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
655 jmc 1.1101 o SingleCpuIO:
656     fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
657     o pkg/seaice:
658 jmc 1.1100 put exchanged variable in (local) common block for MPI+Multi-Threads
659     to work (necessary with exch1, and for now with exch2 too).
660 jmc 1.1099 o verification: to get more experiments tested with mpi, mth and mpi+mth,
661     change tiling of:
662     aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
663     hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
664     update output of exp:
665     exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
666     tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
667     + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
668     (note: output.txt generated on faulks using only 1 tile)
669 jmc 1.1098 o eesupp & mdsio (SingleCpuIO):
670     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
671     parameter "W2_useE2ioLayOut" (read from file "data.exch2").
672     Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
673     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
674     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
675     gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
676 jmc 1.1097 o pkg/exch2:
677     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
678     read parameter file "data.exch2" if it exists; otherwise try default regular
679     cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
680     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
681     with new code (not to be used, just as a backup solution).
682 jmc 1.1098 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
683     in utils/exch2/input.
684 jmc 1.1097
685 jmc 1.1203 checkpoint61n (2009/05/12)
686 jmc 1.1095 o eesupp & mdsio (SingleCpuIO):
687     - move mapping to global io-buffer inside gather_2d/scater_2d: this save
688     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
689     receive real*4 array (instead of real*8) to read/write 32.bit files.
690     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
691     and remove new mapping S/R)
692 jmc 1.1094 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
693     - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
694     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
695     when using exch2. Add S/R to map global io-buffer to global model array.
696     - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
697    
698 jmc 1.1203 checkpoint61m (2009/04/29)
699 jmc 1.1094 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
700     and add 3 other S/R for other types (R4,R8,RS).
701 jmc 1.1092 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
702     o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
703     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
704     - reduce number of macro definitions (keep only those which are used);
705     can always call directly the corrresponding S/R if needed.
706 jmc 1.1094 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
707 jmc 1.1092 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
708     Fixed wrong type of arg in:
709 jmc 1.1094 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
710 jmc 1.1092 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
711     To fix: global_sum of var in common block is wrong (multi-threaded) in:
712     dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
713     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
714 jmc 1.1094 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
715     "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
716 jmc 1.1091 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
717     o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
718     edges are closed (zero depth); might happen with "blank tiles";
719 jmc 1.1094 for now, disabled if using OBCS.
720 jmc 1.1091 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
721 jmc 1.1090 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
722 jmc 1.1091 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
723 jmc 1.1089 to reduce length of 1.D array print in STDOUT.
724 jmc 1.1088 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
725     + use 48 tiles (16x8): this will allow to test "blank tiles".
726     o start to test MPI + multi-threaded (change testreport to skip tests
727     where number of tiles do not match).
728     o genmake2: add option "-omp" to turn on Open-MP ;
729     passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
730 jmc 1.1086 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
731     and keep the original tile numbering. Note: compatible with old
732     W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
733    
734 jmc 1.1203 checkpoint61l (2009/04/07)
735 jmc 1.1085 o Overlaps had been forgotten in calculating ijk keys : fixed
736     o fix cyrus makedepend for gcc 4.4
737 jmc 1.1084 o experiment fizhi-cs-aqualev20:
738     switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
739 jmc 1.1088 and generate new output. Note: new output is much closer to the old
740     one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
741 jmc 1.1084 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
742     o pkg/fizhi:
743     - change to avoid indices going deliberately over array-bounds
744     - remove unnecessary MPI stuff
745     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
746     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
747     does not go over array-bounds and therefore returns reliable output.
748     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
749     this S/R has 4 output arguments, which are used inside "get_alarm";
750     when it is called with the same variable "ndum" in place of several
751     output arguments, this produces weird side effect inside "get_alarm"
752     (e.g., datein=dates(n) is overwritten by timein=times(n) since both
753     datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
754     address) and produces error.
755 jmc 1.1090 o tools/gemake2: (March 27-29 2009)
756     with option "-mpi": link *_mpi files from "MODS" dir (this is what
757     testreport does).
758 jmc 1.1083 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
759 jmc 1.1084 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
760 jmc 1.1083 update lab_sea.lsr & lab_sea.salt_plume results
761 mlosch 1.1079 o pkg/seaice:
762     Major overhaul of the LSOR solver: change discretization from original
763     finite differences to finite volume. The old routine is still in the
764     file seaice_lsr.F and can be turned on with the CPP-flag
765     SEAICE_OLD_AND_BAD_DISCRETIZATION
766     Along with this change, the discretization of the strain rates is changed.
767     The same flag turns on the old discretization in seaice_calc_strainrates.F
768     All verification experiments with seaice are affected (except for
769     seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
770     results by setting the above flag.
771     Further changes involve changes in defaults:
772     - ALLOW_FLOODING is defined and turned on by default
773 heimbach 1.1087 - SEAICEadvSnow = .true. is now the default
774     - SEAICEadvSalt = .true. is now the default
775     - SEAICEadvAge = .true. is now the default
776 mlosch 1.1081 - SEAICE_clipVelocities = .false. is now the default
777     (as per J. Zhang's recommendation)
778 mlosch 1.1079 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
779     is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
780     - seaice_growth: replace computation of UG by a simple copy from wspeed
781    
782 jmc 1.1203 checkpoint61k (2009/03/18)
783 mlosch 1.1078 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
784     seaice_lsr: fixed a few metric terms,
785     affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
786     add more debugging diagnostics
787     seaice_evp: removed superfluous many metric terms of FV discretization
788     of stress divergence
789     affects lab_sea, lab_sea.hb87
790     seaice_ocean_stress: removed superfluous many metric terms of FV discretization
791     of stress divergence for non-evp solver
792     (this part is not tested anywhere)
793     seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
794     they were effectively only half slip
795     affects lab_sea.hb87
796 jmc 1.1082 updated all relevant verification experiments (except lab_sea//output_adm.txt
797     which was left over, but fails at level 7 & 6)
798 mlosch 1.1078
799 jmc 1.1203 checkpoint61j (2009/03/17)
800 mlosch 1.1076 o pkg/seaice: turn a few hard wired parameters into run time parameters
801 mlosch 1.1075 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
802     time in seconds as promised by the usints in seaice_monitor and exf_monitor
803 mlosch 1.1074 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
804     that are not cubed-sphere grids
805 mlosch 1.1073 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
806 jmc 1.1072 o pkg/ctrl:
807     fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
808 jmc 1.1071 o non-hydrostatic (calc_gw.F):
809     fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
810     update output of exp. global_ocean.cs32x15.viscA4
811     o remove backward compatibility for thetaMin,phiMin
812 jmc 1.1070 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
813 mlosch 1.1069 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
814     interpolated wind field not only for curvilineargrid=.true., but also
815     for a rotated grid (rotateGrid=.true.)
816 mlosch 1.1068 o pkg/exf: add capability to bypass interpolation for runoff
817     by setting yet another CPP-flag
818 jmc 1.1070 o eesupp/src, B-grid exchange:
819     add simple (6 tiles, non MPI) CS exch + standard interface S/R.
820 heimbach 1.1067 o autodiff
821     new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
822     allows to switch to single-prec common blocks;
823     corresponding switch occurs in tamc.h, integer isbyte
824     TAF store directivs "byte" and "kind" seem equivalent;
825     Most tamc.h have been updated correspondingly.
826    
827 jmc 1.1203 checkpoint61i (2009/02/13)
828 heimbach 1.1066 o autodiff:
829     fix autodiff_sore/_restore indices for obcs
830     (spotted by I. Hoteit, M. Mazloff)
831 heimbach 1.1065 o pkg/autodiff, pkg/ctrl:
832     Add flag to reduce all tapelev I/O to single-prec.
833     In data.ctrl set
834     doSinglePrecTapelev = .TRUE.
835 jmc 1.1070 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
836     check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
837 mlosch 1.1062 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
838     real fresh water flux (not yet)
839 jmc 1.1060 o pkg/mdsio & rw:
840     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
841     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
842 jmc 1.1058 o pkg/flt:
843     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
844     init_fixed & ini_varia.
845 jmc 1.1059 - clean-up & simplify linear interpolation S/R:
846     move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
847     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
848 jmc 1.1060 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
849 jmc 1.1061 - add vert. coordinate & horiz. indices to output files.
850     - change vertical position in initial condition, from index to depth [m].
851 jmc 1.1063 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
852     (easier to get to a curvilinear grid) ; delX,delY no longer used.
853 dfer 1.1057 o pkg/ggl90: a few modifications:
854     - fix bottom boundary condition, and interpolation of KappaE
855     near top and bottom
856     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
857     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
858     - add a few options for mixing-length upper limit (--> mxlMaxFlag)
859 jmc 1.1056 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
860     (maintain temporary backward compatibility, until next checkpoint)
861    
862 jmc 1.1203 checkpoint61h (2009/01/27)
863 jmc 1.1054 o pkg/diagnostics with "periodic averaging diagnostics":
864     fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
865 jmc 1.1053 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
866 mlosch 1.1052 o pkg/obcs: fix loop ranges for balancing code
867 jmc 1.1051 o pkg/flt:
868     - improve criteria for finding which tile owns a float.
869     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
870 dfer 1.1050 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
871     aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
872     with ocean biogeo)
873 jmc 1.1049 o pkg/flt:
874     - do some cleaning and fix the restart ;
875     - add output.txt in flt_example/results to get this pkg tested.
876     o genmake2: add an EXTENDED_SRC option and flag.
877     for now, cannot be turned on on command line (only through genmake_local)
878 jmc 1.1048 o pkg/mdsio: read/write vector:
879     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
880 jmc 1.1049 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
881 jmc 1.1048 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
882     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
883     (drop to 4 digits matching for grad). But this test does not look very
884     reliable (was already failling on eddy, fc5, at 6.digits). Update output.
885    
886 jmc 1.1203 checkpoint61g (2008/12/29)
887 jmc 1.1046 o pkg/flt:
888     - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
889     + make OPTIONS file more standard.
890     - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
891     - fix _BYTESWAPIO CPP-Flag
892     - standard reading of file-parameter "data.flt"
893 jmc 1.1047 - fix argument list of S/R FLT_RESTART
894 jmc 1.1046 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
895 mlosch 1.1045 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
896 mlosch 1.1044 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
897     a still unfixed compiler/optimization bug
898    
899 jmc 1.1203 checkpoint61f (2008/11/21)
900 jmc 1.1042 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
901     update results of global_ocean.cs32x15.icedyn test.
902 jmc 1.1041 o move getcon.F from model/src to pkg/fizhi.
903 jmc 1.1040 o pkg/exf: add parameter for extrapolation of temp up to the surface
904     and option to prevent negative evap (in bulk_largeyeager04 only).
905 jmc 1.1039 o Prather Advection scheme: fix tracer conservation for divergent flow
906     (e.g., when using NonLin Free-Surface).
907 dfer 1.1038 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
908 jmc 1.1037 o gmredi (Visbeck-variable-K):
909     - add more parameters to Visbeck-variable-K.
910     - use a 5 points average for dSigmaR in Visbeck-K calculation
911     (more "homogenous": same stencil and same weights as in dSigmaH)
912     - update output of ideal_2D_oce experiment.
913 mlosch 1.1034 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
914     (#undef REAL4_IS_SLOW)
915     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
916     coordinate variable
917     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
918     (surface forcing fields), removes some of the functionality
919     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
920     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
921     probably not all: copy _RS surface flux fields to RL field before
922     calling DIAGNOSTICS_FILL
923 mlosch 1.1035 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
924     real*4 (CALL EXCH_*_RS) versions.
925 jmc 1.1036 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
926     (generate new output).
927 mlosch 1.1034
928 jmc 1.1203 checkpoint61e (2008/10/23)
929 jmc 1.1032 o gmredi (Visbeck-variable-K):
930     - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
931     - change computation of Visbeck-K where Slope > Smax :
932     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
933     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
934 jmc 1.1031 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
935     to be the same as with Z-coord. (i.e., m/s & no-units respectively).
936     o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
937 jmc 1.1030 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
938 jmc 1.1032 does not become too large (to avoid precision problems in implicit-diffusion
939 jmc 1.1030 solver); update ideal_2D_oce output.
940 dfer 1.1028 o pkg ggl90:
941     - in ggl90_cal.F: compute only one set of visc/diff, used to
942     step forward TKE/T/S/momentum
943     - default value of GGL90viscMax/GGL90diffMax larger and equal (to
944     have Prandlt =1)
945 jmc 1.1032 o gmredi (fm07):
946 jmc 1.1029 - add lower limit on Transition layer thickness + lower limit on 1/lambda
947 jmc 1.1027 - allow to set few more params from data.gmredi
948 dfer 1.1026 o pkg ggl90:
949     - add missing sqrt(2) factor in computation of mixing length
950     scale in ggl90_calc.F
951     (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
952    
953 jmc 1.1203 checkpoint61d (2008/09/25)
954 heimbach 1.1025 o adjoint modifs
955     - adapt to new field rhoInSitu
956     - allow to revert from StoreDynVars2D, StoreDynVars3D
957     to individual fields
958     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
959 jmc 1.1024 o store 3-D (in-situ) density in commom block (DYNVARS.h)
960     - save 1 rho computation.
961     - no longer modify T & S inland when using down_slope pkg.
962 jmc 1.1023 o gad_som : allow to switch to SOM advection for T & S without corresponding
963     pickup files (using new S/R: MDS_CHECK4FILE).
964     o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
965     (for useSingleCpuIO to work in multi-threaded)
966 mlosch 1.1022 o pkg/shelfice:
967     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
968     with SHELFICEtopoFile in data.shelfice
969     - move code for reading ice shelf topography and modifying hFacC into separate
970     subroutines of the shelfice package
971     - separate initialisation of "fixed" and "variable" variables
972     - kTopC is not (yet) replaced by kSurfC, although this is possible
973 jmc 1.1023 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
974 jmc 1.1020 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
975     and rename:
976     ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
977     ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
978     o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
979    
980 jmc 1.1203 checkpoint61c (2008/08/30)
981 jmc 1.1018 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
982     to add mass source/sink of fluid in the interior (3-D generalisation
983     of oceanic real-fresh water flux).
984     o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
985 jmc 1.1017 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
986 jmc 1.1016 o new pkg: down_slope
987     density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
988     - presently, modify T & S inland (dwnslp_calc_rho.F).
989     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
990     - implementation for ocean in P-coords not tested.
991     - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
992     o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
993 jmc 1.1015 (to facilitate conversion of oceanic pkg to p-coordinate).
994 jmc 1.1014 o change FIND_RHO to FIND_RHO_2D :
995     pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
996     o new pkg: cheapaml
997    
998 jmc 1.1203 checkpoint61b (2008/08/05)
999 jmc 1.1011 o exch2:
1000 jmc 1.1012 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
1001     - no longer depend on the order sequence (N,S,E,W).
1002     - 3rd exchange no longer needed (tested with 24 tiles).
1003     - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
1004     - exch_UV_A-grid readily available (but not yet tested).
1005     comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
1006     (both are no longer needed) in exch_uv: no effect in forward run; but
1007     get truncation error differences with adjoint exch.
1008     o exch2:
1009 jmc 1.1011 - change index-bounds storage (moved from target to local tile,
1010     more intuitive this way) ; rename/remove some variables.
1011 jmc 1.1012 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
1012 jmc 1.1011
1013 jmc 1.1203 checkpoint61a (2008/07/29)
1014 jmc 1.1009 o exch2/matlab-topology-generator:
1015     fix bug in index bounds for N-S internal exchange (hard to tell if this
1016     had any effect on the solution).
1017 mlosch 1.1008 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
1018     is exceeded
1019 mlosch 1.1007 o testreport: modify syntax of awk, so that it works also with
1020     awk, and not only with nawk and gawk
1021    
1022 jmc 1.1203 checkpoint61 (2008/06/24)
1023 heimbach 1.1005 o autodiff
1024     Change default for TAF usage by removing argument '-nonew_arg'
1025     This changes TAF subroutine argument list (ordering of active var.)
1026     Omission of this flag leads to incompatibility w.r.t. TAMC
1027     To restore TAMC-compatibility, need following modifs:
1028     * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
1029     * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
1030     Tested TAF version is 1.9.22
1031     N.B.: exch2 hand-written adjoint code currently not TAMC compatible
1032    
1033 jmc 1.1203 checkpoint60 (2008/06/19)
1034 heimbach 1.1004 --->>> This is the last checkpoint for which generating the adjoint
1035     --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
1036     --->>> by default.
1037     --->>> Future checkpoints will ommit this flag by default.
1038 jmc 1.1003 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
1039 gforget 1.1002 o pkg/grdchk: Add gradient check to etan0 perturbations.
1040 gforget 1.1001 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
1041 gforget 1.1000 o pkg/autodiff: more flexibility in zeroadj.
1042     model/src: modifying do_oceanic_phys.F accordingly.
1043 gforget 1.999 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
1044     o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
1045     special setup of gmredi for which the adjoint is stable
1046     enough for parameter optimization.
1047 gforget 1.998 o bridging the gap between eddy stress and GM.
1048     -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
1049     along with a change in CPP option (now ALLOW_EDDYPSI).
1050     -> when using GM w/ GM_AdvForm:
1051     The total eddy streamfunction (Psi = eddyPsi + K x Slope)
1052     is applied either in the tracer Eq. or in momentum Eq.
1053     depending on data.gmredi (intro. GM_InMomAsStress).
1054     -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
1055     The key modifications are in model/src/taueddy_external_forcing.F
1056     pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
1057 jmc 1.1003
1058 jmc 1.1203 checkpoint59r (2008/05/29)
1059 jmc 1.996 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
1060     from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
1061     fix option to read coriolis(@ cell-corner) from files with CS-grid.
1062 mlosch 1.995 o pkg/mnc: add some attributes to standard 1D-coordinate variables
1063 mlosch 1.993 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
1064     mass points, when using mnc for output
1065     - add runtime parameter (missing_value, missing_value_int) to override
1066     default (which is the value of getcon('UNDEF'))
1067     o pkg/mnc: prepare mnc for the actual use of missing values with the
1068     diagnostics package: small fix in mnc_cw_readwrite.template and more
1069     initialisation of never used fields
1070 mlosch 1.994 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
1071     versions
1072     o pkg/thsice/thsice_ini_vars.F added default initial values so that
1073     thermodynamics sea ice solver does not blow up when some initial fields
1074     are missing.
1075 jmc 1.991 o move from external_forcing_surf.F to ini_forcing.F
1076     the p-coord. hack consisting in using pLoad to set phi0surf ;
1077     update output of tutorial_global_oce_in_p (affected @ truncation level).
1078 dfer 1.990 o Freshen up a bit hs94.1x64x5, notably:
1079 mlosch 1.994 remove rotationPeriod and tRef=5*0. (adjoint only), and add
1080     exactConserv=.TRUE.
1081 jmc 1.989 o pkg/generic_advdiff:
1082     change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
1083     applies to files where Temperature & Salinity 2nd Order moments are used.
1084 jahn 1.988 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
1085     this uses a dynamically allocated internal state data structure
1086     (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
1087     and requires a fortran 90 compiler
1088    
1089 jmc 1.1203 checkpoint59q (2008/05/06)
1090 jmc 1.986 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
1091     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
1092 dfer 1.985 o Refresh tutorial_global_oce_biogeo, notably:
1093     - change bathymetry (put back seamounts in ACC, use hFacs)
1094     - change EOS (POLY3 --> JMD95Z)
1095     - use Bryan-Lewis vertical diffusivity
1096     - use multidimensional advection
1097     - remove old virtual virtual in dic pkg, now done through ptracer pkg
1098     - change a couple of parameters in dic pkg
1099 gforget 1.984 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
1100 mlosch 1.982 o pkg/obcs: change default to OBCSfixTopo = .true.,
1101 mlosch 1.983 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
1102     - replace "debugMode" with "debugLevel .GE. debLevB"
1103 gforget 1.981 o implementation of TAF directives for gchem,cfc,dic
1104 jmc 1.980 o remove "exp5" (replaced by tutorial_deep_convection).
1105 mlosch 1.979 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
1106     this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
1107     the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
1108 mlosch 1.982 --> changes results in exp4, seaice_obcs
1109 jmc 1.980 o tutorial_deep_convection :
1110 jmc 1.978 update the set-up and increase resolution and domain size ; start
1111     from pseudo initial conditions = output at t=120mn in order to see
1112     something happening when running testreport.
1113 mlosch 1.976 o pkg/seaice: add os7mp as an advection scheme
1114     add check for advection schemes
1115 mlosch 1.977 add a flag for restoring T and S underneath sea ice
1116 mlosch 1.975 o pkg/my82: add netcdf-support and diagnostics
1117 dfer 1.974 o thsice pkg:
1118 mlosch 1.979 - Now hsMax limits snow height by turning it into ice following
1119 dfer 1.974 flooding scheme (and now conserving energy)
1120     - Slight rewriting of the formula in thsice_calc_thick.F
1121     - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
1122 jmc 1.980 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
1123 dfer 1.974
1124 jmc 1.1203 checkpoint59p (2008/04/10)
1125 jmc 1.973 o gchem / dic / cfc :
1126     - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
1127     - add new parameter files: "data.dic" & "data.cfc" ;
1128     - various re-arrangement in initialisation & header file ;
1129     - fix tutorial_global_oce_biogeo for multi-threaded test.
1130     o pkg/dic: test for "pickup_dic" file when restarting ;
1131     if no pickup-file, can restart with a re-initialised pH (same as it did
1132 jmc 1.972 before) providing pickupStrictlyMatch is set to False.
1133 jmc 1.971 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
1134     + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
1135 jmc 1.970 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
1136     and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
1137     o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
1138     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
1139     (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
1140 jmc 1.969 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
1141     scheme to use for vorticty-term ;
1142     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
1143     (with default selectVortScheme, return to original discretisation)
1144     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
1145 mlosch 1.968 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
1146 jmc 1.967 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
1147     bottom ; only used with variable horizontal viscosity and non-hydrostatic.
1148     also fix diagnostics VISCAHW & VISCA4W.
1149    
1150 jmc 1.1203 checkpoint59o (2008/03/07)
1151 jmc 1.965 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
1152 mlosch 1.964 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
1153     move a few statemens out the main loop into separate loops
1154 mlosch 1.962 o pkg/shelfice:
1155     - sort out freshwater flux; convert freshwater fluxes to mass fluxes
1156     (kg/m^2/s), does not break tests, because in verification/isomip,
1157     rhoConstFresh=rhoConst (by accident)
1158 mlosch 1.963 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
1159     - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
1160     new file model/src/seawater.F, so that they are available for all pkgs.
1161     - convert potential temperature into in-situ temperature. This changes the
1162     isomip tests => update tests
1163 mlosch 1.961 o add a flag writePickupAtEnd (default=true) to be able to suppress
1164     writing a pickup at the last timestep
1165 jmc 1.966 o tools/mpack-1.6 :
1166     - disable automake (not working) and autoconf (not needed).
1167     - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
1168     also cleaner with much less compilation warnings.
1169 gforget 1.960 o pkg/profiles:
1170     rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
1171     (for "less than 32 characters name" compiler requirement)
1172 dimitri 1.959 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
1173     conditions that have a different sampling frequency than S/T/U/V obcs
1174 jmc 1.958 o pkg/diagnostics (stats-diags):
1175     - fix global Min/Max in case 1 processor get only empty tiles
1176 mlosch 1.957 o genmake2: replace (4 times)
1177     make genmake_tc_1.o >> genmake_warnings 2>&1
1178     with
1179     COMM="$CC $CFLAGS -c genmake_tc_1.c"
1180     echo $COMM >> genmake_warnings
1181     $COMM >> genmake_warnings 2>&1
1182     to make genmake2 always see the value of CC as specified in the optfile.
1183 jmc 1.956 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
1184     - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
1185     - modify verification advect_cs test to test SOM-advection on CS-grid.
1186 gforget 1.955 o pkg/ctrl:
1187     - Rewrite of ctrl_map_ini_ecco.F,
1188     introducing a generic routine (ctrl_map_ini_gen.F).
1189     - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
1190 jmc 1.956
1191 jmc 1.1203 checkpoint59n (2008/02/09)
1192 jmc 1.953 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
1193     number in dedicate array "hdiag":
1194     - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
1195     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
1196     - many small changes (integer format) for large number of diagnostics
1197     - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
1198     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
1199 mlosch 1.952 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
1200     usingSphericalGrid, this allows to define the rotated grid coordinates
1201     via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
1202     geographical coordinates according to the inverse of the rotation defined
1203     by the Euler angles, so that Coriolis parameter and online-interpolation by
1204     exf works with the geographical coordinates on XC/YC/XG/YG.
1205     Naturally, this feature does not work with all packages, so some
1206     combinations are prohibited in config_summary (flt, flt_zonal, ecco,
1207     profiles), because there the coordinates are assumed to be regular
1208     spherical grid coordinates.
1209 gforget 1.951 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
1210     - introduce isopycnal diffusion coefficient control.
1211     o tools/adjoint_options:
1212     - additional control vector components.
1213 mlosch 1.950 o pkg/mnc: have mnc create marginally meaning full coordinate variables
1214     (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
1215 jmc 1.948 o pkg/mypackage:
1216     - add example of read/write pickup for state-var ;
1217     - add entry points to the main code for state-vars diags & write-pickup.
1218 dimitri 1.946 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
1219     transitions for useExfYearlyFields
1220 mlosch 1.947 - add new subroutine that determines the file to read from for
1221     use*YearlyFields = .TRUE. and .FALSE.
1222 mlosch 1.949 - add a verification experiment to global_with_exf that tests
1223     useExfYearlyFields with USE_EXF_INTERPOLATION defined
1224 mlosch 1.945 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
1225     analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
1226     subroutines (which could be generated from a template, because they are
1227     almost identical), for now they are included in obcs_prescribe_read.F for
1228     simplicity
1229 mlosch 1.943 o pkg/exf:
1230     - add a little more diagnostic to exf_interp_read (in analogy to
1231     mds_read_field, can be turned off with debugLevel < debugLevA=1)
1232     - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
1233 mlosch 1.944 ugly but fast by unrolling short inner loops, inserting a unroll=8
1234     directive in routine lagran, and splitting a loop and making do while the
1235     outermost loop (the latter requires the intoduction of index arrays)
1236 dimitri 1.942 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
1237 dimitri 1.941 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
1238     http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
1239 dimitri 1.940 o verification/seaice_obcs: updated for restart test and latest options
1240 mlosch 1.939 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
1241     ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
1242     for now this is only available for the C-grid code and also within
1243     #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
1244    
1245 jmc 1.1203 checkpoint59m (2008/01/14)
1246 dimitri 1.936 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
1247     and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
1248 dimitri 1.937 o gad_som : fix flux output (& diagnostics) to have same units as other
1249     advection scheme fluxes (was previously multiplied by deltaT).
1250 dimitri 1.933 o added verification/seaice_obcs both to test seaice open boundaries
1251     and to provide an example matlab scrpt for generating them
1252     o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
1253 atn 1.931 o pkg/salt_plume: clean up salt_plume_frac.F to
1254     remove redundancy in PlumeMethod 1 and 4
1255 atn 1.930 o pkg/kpp: added saltplume diagnostics
1256 dimitri 1.929 o pkg/obcs and pkg/seaice:
1257     - do not set uice and vice to zero when OB*icefile are unspecified
1258     - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
1259     - moved seaice tracer obcs after call to seaice_growth
1260 dimitri 1.927 o pkg/salt_plume: added various options for salt plume depth
1261     criterion and for vertical distribution of the salt
1262 jmc 1.928
1263 jmc 1.1203 checkpoint59l (2007/12/18)
1264 jmc 1.925 o pkg/ptracers: new version of ptracers pickup:
1265     read meta file and write only fields which are needed to restart.
1266     ( same logic as main pickup file ; also using pickupStrictlyMatch )
1267 dimitri 1.924 o pkg/seaice:
1268 mlosch 1.923 - add timescale for melting due to warm mixed layer as a means of
1269     setting SEAICE_availHeatFrac more conveniently
1270     - add a CPP-flag/runtime parameter check for flooding algorithm
1271 dimitri 1.924 - reformulated availHeat in seaice_growth.F to be independent of AREA
1272 mlosch 1.923 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
1273     unit changes
1274 dimitri 1.921 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
1275 mlosch 1.919 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
1276     SX vector computer.
1277 dimitri 1.920 o pkg/seaice:
1278     - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
1279     seaice forcing fields can now be read only through pkg/exf
1280     - removed some unused halos
1281 jmc 1.917 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
1282 dimitri 1.922 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
1283     or U/VICE from U/VWIND before computing U/VSTRESS
1284 dimitri 1.916
1285 jmc 1.1203 checkpoint59k (2007/11/30)
1286 dimitri 1.914 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
1287     dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
1288 jmc 1.913 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
1289 jmc 1.925 all experiments pass when compile with un-initialised var. checking option.
1290 dimitri 1.912 o added pkg/salt_plume
1291 jmc 1.911 o script to test restart (for now, in MITgcm_contrib/jmc_script)
1292     o pkg/seaice: new read/write pickup version.
1293     read meta file and write only fields which are needed to restart.
1294     ( same logic as main pickup file ; also using pickupStrictlyMatch )
1295 mlosch 1.910 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
1296 jmc 1.909 o lab_sea.hb87: modify the domain & update output.hb87.txt :
1297     lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
1298     at j=1 & j=Ny+1 : this case is not treated correctly in the restart
1299     process. Fixed here by closing the domain at the Northern boundary.
1300     o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
1301     o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
1302     a set of consecutive levels in/from a 3-D array.
1303 jmc 1.908 o pkg/ptracers:
1304 jmc 1.909 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
1305 jmc 1.908 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
1306    
1307 jmc 1.1203 checkpoint59j (2007/11/09)
1308 jmc 1.906 o in pkgs: dic, obcs, offline, rbcs:
1309     standard way to compute coeff. for time interpolation between 2 time reccords
1310     which retains full precision (& make results less dependent on compiler).
1311     update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
1312 mlosch 1.905 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
1313     packages instead of reading ice cover and wind speed separately
1314 jmc 1.904 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
1315     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
1316     to allow to compile customized code before the update)
1317 jmc 1.903 o cleaning-up:
1318     - fix CPP instruction syntax in pkg/obcs
1319     - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
1320     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
1321     - fix some threads issue in IO parts.
1322 dfer 1.901 o pkg/dic:
1323     - add tons of "_d 0" (--> much better testreports !)
1324     and then update outputs of tutorial_global_oce_biogeo
1325 jmc 1.900 o pkg/mom_fluxform:
1326     add a special version of momentum advection intended to conserve momentum
1327     next to a bathymetry step or a coastline edge. (default = off = #undef)
1328 jmc 1.898 o new read/write pickup version:
1329     - for now, only implemented for main (mdsio) pickup file.
1330     - write out only what is needed to restart; merge pickup_nh , pickup_ph
1331     and main pickup together.
1332     - read meta file; read only what is needed to restart; stop if a field
1333     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
1334     if it make sense (even if the restart is not perfect).
1335     - if no meta file, assume that pickup to read corresponds exactly to
1336     a pickup that would currently be written.
1337     - read pickup written in the old format (until checkpoint59i) if it
1338     recognizes an old meta file (no field-list).
1339     - add a meta file in exp. which starts from a pickup: 2 cases:
1340     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
1341     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
1342     b) a meta file describing the content of the associated pickup file
1343     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
1344     o pkg/mdsio & pkg/rw:
1345     - new routine to read a meta file ; new set of routine to read
1346     Multiple-fields file (with meta file).
1347 dimitri 1.899 o added open boundary conditions capability for seaice
1348     HSNOW, HSALT, UICE, and VICE
1349 dimitri 1.897
1350 jmc 1.1203 checkpoint59i (2007/10/21)
1351 heimbach 1.895 o adjoint:
1352     * fix multiDimAdvection adjoint
1353     (partial recomputation problem by TAF for fVerT(:,:,kDown)
1354     and comlev1 size definition (maxpass vs. max. number of tracers)
1355     * verification/global_ocean.90x45x15 adjoint now tests
1356     NLFS and multiDimAdvection using DST3 (=30)
1357     * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
1358 jmc 1.894 o pkg/kpp: add "_d 0" to real constant (if missing);
1359     update output of exp: natl_box (10.digits); vermix (std, 7.digits)
1360     and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
1361 jmc 1.893 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
1362     for internal parameters related to restart process (formerly from PARAMS.h)
1363     and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
1364     o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
1365     as argument. (only atm2d & obcs write_pickup have not yet been updated)
1366 jmc 1.892 o pkg/monitor:
1367     - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
1368     - fix mon_stats_rs (statistics over the full domain, even where field is zero)
1369     - account for deep Atmosphere factor and density factor (anelastic)
1370 dimitri 1.891 o added open boundary conditions capability for seaice HEFF and AREA
1371 mlosch 1.890 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
1372     thermodynamics
1373     - requires a little reorganization, which affects the testreport results
1374     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
1375     so that now the conservative form is tested
1376     - add a few comments
1377 jmc 1.892 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
1378 mlosch 1.888 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
1379 mlosch 1.887 o add new diagnostics to seaice: advective, diffusive fluxes (only for
1380     multidim-advection, for scheme 2 they are not filled) and transports,
1381     thermodynamic growth rates
1382 jmc 1.902 o change units of EmPmR (inside the code, + within coupling interface)
1383     from m/s to kg/m2/s (mass flux) but leave input file unchanged.
1384     Affects results @ truncation level (cg2d match) and update output of
1385     experiments: lab_sea(6), global_ocean.90x40x15(10),
1386 jmc 1.886 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
1387     + adjoint results: global_ocean_ebm(11) and lab_sea (12).
1388 jmc 1.902 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
1389 jmc 1.886 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
1390    
1391 jmc 1.1203 checkpoint59h (2007/09/29)
1392 mlosch 1.884 o pkg/exf:
1393     - improve vectorization by moving if-statement out of loops in
1394     exf_mapfields, exf_radiation
1395     - exf_bulkformulae.F: introduce 2D fields and vectorize code
1396 dimitri 1.881 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
1397 jmc 1.880 o testreport:
1398     - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
1399     monitor & update offline_exf_seaice exp. output.
1400     - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
1401 mlosch 1.879 o pkg/seaice:
1402     - bug fix in the evp solver: boundary conditions were affected be
1403     masking of zMax/zMin (changes results)
1404     - minor bug fix in boundary conditions in seaice_calc_strainrates
1405     (changes results for no_slip)
1406     - seaice_lsr.F: make interpolation of eta dependent on boundaries
1407     - replace hardcoded lower limit for zeta (zMin) by runtime parameter
1408     - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
1409     stress formulation and no-slip boundary conditions
1410 jmc 1.878 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
1411     in gad_calc_rhs.F ; add few safety stops in initialisation phase.
1412 dimitri 1.877 o pkg/seaice: a first HSALT time stepping equation has been checked in
1413 dimitri 1.875 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
1414     in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
1415     without requiring DO-IF statements
1416 jmc 1.876 o pkg/thsice:
1417     use continuous power-law function for partition of energy between lateral
1418     melting/freezing and thinning/thickening ; old code using step function
1419     still available with #undef THSICE_FRACEN_POWERLAW
1420     update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
1421     o testreport: change AD testing : check against results/output_adm.txt
1422     using same scripts as for forward test.
1423 dimitri 1.875
1424 jmc 1.1203 checkpoint59g (2007/09/17)
1425 jmc 1.873 o adjoint testing: in preparation for changing testreport:
1426     - output format: cost and grad written on separated lines
1427     - ad output results in directory "results" (instead of "results_ad")
1428 dimitri 1.872 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
1429 dimitri 1.871 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
1430 gforget 1.870 o pkg/ecco: allow user defined cost function contributions
1431 jmc 1.869 o testreport:
1432     Allow to choose (per experiment) the list of tested output variables
1433     and the main variable (used to issue a pass/FAIL ) ;
1434     - for now, done by adding the specific list in file: [exp]/input/tr_checklist
1435 jmc 1.873 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
1436 jmc 1.869 Also modify printing of summary:
1437     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
1438     b) echo the list of tested variables in the individual summary.txt of
1439     each experiment.
1440 jmc 1.868 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
1441     threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
1442     (but still depend on the tile decompostion of the domain).
1443 mlosch 1.867 o pkg/seaice: change a discretization detail to make the B-grid code
1444     "more symmetric". This change is likely to remove all "ridges/leads" that
1445     where quasi-aligned with the grid in B-grid solutions. It may also be
1446     the solution to the stress coupling issues with the B-grid.
1447 jmc 1.866 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
1448     remove .cvsignore from input dir. (since testreport no longer run here).
1449 jmc 1.865 o pkg/thsice:
1450 jmc 1.866 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
1451 jmc 1.865 - fix reshaping of sea-ice just after advection:
1452     melt all the ice only if ice-volume is too small.
1453     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
1454     prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
1455     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
1456 jmc 1.864 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
1457     tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
1458 jmc 1.863 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
1459     forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
1460     (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1461     and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1462     of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1463     -> update output.txt
1464     o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1465     this affects truncation error: -> update output.txt of exp:
1466     global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1467     ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1468    
1469 jmc 1.1203 checkpoint59f (2007/08/21)
1470 gforget 1.861 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1471     o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
1472     a bounded range (in forward mode)
1473 gforget 1.860 o pkg/ecco, ctrl, autodiff and mom_common:
1474     internal parameter controls, completements of implementations
1475 jmc 1.859 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1476 jmc 1.862 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1477     (not seem any difference in testing results).
1478 jmc 1.859 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1479     at face corners.
1480 jmc 1.858 o pkg/generic_advdiff:
1481     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1482     loop range indices for computing vertical advection tendency
1483     and do the calculation in the interior only (no overlap) ;
1484     for now, only implemented for SOM advection (to save CPU time).
1485     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1486 heimbach 1.855 o exch2 adjoint
1487     First set of changes:
1488     - add exch2 hand-written adjoint templates
1489     - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1490     This will require cleanup in pkg/autodiff/*.F
1491     (changed routines currently kept separate in verif. code/)
1492     - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1493     that used to hide exch2 or cubed-sphere specific code
1494     (commented via 'cph-exch2')
1495 dimitri 1.856 o pkg/seaice
1496     - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1497 jmc 1.857 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1498     output of global_ocean.cs32x15.thsice .
1499 heimbach 1.855
1500 jmc 1.1203 checkpoint59e (2007/07/26)
1501 jmc 1.853 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1502     for B-grid vector (not yet tested) and C-grid vector (<- only used
1503     when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1504 dimitri 1.852 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1505     (#ifdef ALLOW_SALT_PLUME)
1506 dimitri 1.851 o gather_2d/scatter_2d: removed halo regions
1507 jmc 1.845 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1508     scheme and the corresponding test case (under front_relax dir). For now,
1509     only available with Skew-flux form and not yet tested in realistic set-up.
1510 heimbach 1.847 adjoint: store directives updated, but gradient checks deteriorated,
1511     so maybe GM/Redi adjoint is now broken.
1512 heimbach 1.844 o seaice adjoint
1513     * add AREA, HEFF, HSNOW as control variable
1514     (should not change lab_sea results)
1515     * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1516 dimitri 1.848 o pkg/seaice:
1517     * added computation of saltFlux in seaice_growth;
1518     For time being, sea ice salinity is assumed constant
1519     contribution of snow flooding to freshening of sea ice is neglected.
1520     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1521     defaults to 0.0 in order to maintain backward compatibility.
1522     Typical values for SEAICE_salinity are 4 to 10 g/kg.
1523     * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1524     * added SEAICE_availHeatFrac, which specifies fraction of surface level
1525     heat content used to melt or grow ice
1526 dimitri 1.849 * commented out cap of HICE: it helps keep ice thinner
1527     * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1528 dimitri 1.850 * applied OBCS T/S mask to HEFFM sea ice mask
1529 heimbach 1.844
1530 jmc 1.1203 checkpoint59d (2007/06/21)
1531 jmc 1.842 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1532     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1533     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1534     o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1535     and change default value of parameter "GM_Small_Number";
1536     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1537     global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
1538     tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1539 gforget 1.841 o pkg/ecco: cost function when applying pkg/smooth to controls
1540     o pkg/ctrl: add forcingPrecond run time parameter
1541 mlosch 1.839 o pkg/seaice:
1542     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1543     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1544     changes verification/lab_sea
1545     - rearrange implicit part of u-equation in LSR solver to make it easier to
1546     read, understand, and debug. This causes changes at the truncation level.
1547     - fix (serious) bug in the boundary conditions (sign error in the implicit
1548     part) of the LSR solver. Changes all LSR results.
1549 dimitri 1.840 - fixed problem with HSNOW initialization to avoid thick snow when AREA
1550     is initilized with small values - does not change lab_sea results.
1551     - added HsnowFile initialization capability
1552 gforget 1.838 o pkg/smooth: addition to model/src and pkg/ctrl so allow
1553     initialization of pkg/smooth and application to control vector
1554 mlosch 1.837 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1555 gforget 1.836 o dependencies: pkg/profiles requires pkg/cal
1556 gforget 1.835 o pkg/profiles:
1557     - added option ALLOW_PROFILES_GENERICGRID
1558     -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1559     that interpolation information (grid points and coefficients) is provided
1560     within the netcdf input files.
1561     -> sample matlab scripts can be found in MITgcm_contrib/gael
1562     that allow you to prepare netcdf input files.
1563     - also modified: cleaner include statements, cleaner error print statements,
1564     cleaner stops when error, and more tests of the netcdf input files consistency.
1565 jmc 1.834 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1566 mlosch 1.830 o pkg/seaice:
1567 mlosch 1.833 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1568     requires a new routine: seaice_diagnostics_fill.F
1569 mlosch 1.832 - make sure that seaice does not move if not forced (pressure replacement
1570     method, Hibler and Ip, 1995), changes results
1571 mlosch 1.830 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1572     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1573     It is turned off by default (=-1.), because it changes the results.
1574 mlosch 1.831 - make it possible to read AREA from a file, too.
1575 mlosch 1.830
1576 jmc 1.1203 checkpoint59c (2007/06/04)
1577 jmc 1.828 o add S/R and diagnostics for oceanic mixed-layer depth
1578     o move GMRedi call after all vertical mixing schemes (including KPP)
1579     o pkg/thsice:
1580     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1581     (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1582 mlosch 1.824 o pkg/obcs:
1583     - bug fix for balance code
1584 mlosch 1.822 o pkg/seaice:
1585 mlosch 1.825 - allow values of SEAICE_elasticParm > 1
1586 mlosch 1.826 - add new parameter SEAICE_evpTauRelax as an alternative
1587     to SEAICE_elasticParm
1588 mlosch 1.825 - make lsr boundary conditions free slip (by default), changes result
1589 mlosch 1.823 - add code for no slip boundary conditions for lsr
1590 mlosch 1.822 - set minimum of zeta to zero (and not 4e8) (changes results)
1591 mlosch 1.826 - add a cap on AREA after advecting AREA if seaice_growth is not called
1592 jmc 1.821 o change calculation of Visbeck K:
1593     - no longer depend on tapering scheme; instead, compute slope (limited
1594     by GM_maxSlope). this is equivalent to what was comuted before with
1595     clipping or linear tappering.
1596 jmc 1.828 - fix vertical averaging (wrong by 1/2 level)
1597 jmc 1.821 - leave the old version (but will not be maintained) within
1598     #ifdef OLD_VISBECK_CALC / #endif
1599 jmc 1.828 - update output of exp. ideal_2D_oce
1600 mlosch 1.820 o change error catch in calc_r_star to improve vectorization
1601 jmc 1.819 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1602     add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1603 heimbach 1.827 o adjoint:
1604     Re-organized adjoint checkpointing according to Matt Mazloff
1605     (but with modifs/completions/cleanups)
1606     Storing is now bundled into large arrays to optimized I/O
1607     (and second step in cleanup of the_main_loop)
1608 jmc 1.819
1609 jmc 1.1203 checkpoint59b (2007/05/16)
1610 jmc 1.818 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1611     - export/import (between ocean & coupler) fields needed for ocean DIC.
1612 mlosch 1.817 o pkg/seaice:
1613     - get rid of three more exchanges seaice_calc_viscosities (required
1614     different loop boundaries in seaice_lsr and seaice_ocean_stress)
1615     - bug fix in seaice_ocean_stress (update of lab_sea required)
1616     - reduce loop boundaries to necessary minimum also in seaice_evp
1617     - go back to the old way of computing deltaC/Z as the adjoint likes that
1618     better
1619 dfer 1.816 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
1620     passive tracer to an Age Tracer) + update output.txt
1621 jmc 1.814 o pkg/exf:
1622 jmc 1.815 - implement A-grid / C-grid selection for wind-stress input files.
1623     - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
1624     for now, in exf_bulk_largeyeager04.F only :
1625     - change implementation for case where windspeed + 2. components wind-stress
1626     are read-in. AND use rhoConstFresh to convert evap.
1627     o pkg/seaice:
1628     - use correct EXCH_UV for wind-forcing (on A-grid).
1629     - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
1630     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
1631     o pkg/exf:
1632 jmc 1.814 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
1633     EXF_INTERPOLATION:
1634     - merge global_with_exf/code version of exf_interp_read.F
1635     to the main code ;
1636     - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
1637     reading the file ; Important: This options needs to be defined to recover
1638     previous code.
1639     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
1640     - no longer loose real*8 precision along the way when using exf_iprec=64.
1641 mlosch 1.811 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
1642 mlosch 1.813 - change discretisation of evp-solver in order to avoid another exchange
1643     (changes lab_sea) and clean up a little
1644     - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
1645     help the adjoint (this also changes the results slightly)
1646     - add a few "_d 0" where they had been missing in seaice_evp.F
1647     - cleaning up: remove unused seaice_calc_rhs.F
1648 jmc 1.810 o pkg/exf: some cleaning-up:
1649     - change various "constants" into runtime parameters
1650     - cleaned-up Large&Yeager04 routine which should eventually
1651     replace exf_bulkformulae.F (changed names of S/R and CPP)
1652     and merged various ALLOW_ATM_WIND options
1653     only used with thsice pkg (in thsice_get_exf.F):
1654     - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
1655     which are used when useStabilityFct_overIce=TRUE (= the default)
1656     - change default values of ice & snow emissivity and scale downward LW
1657     by ice & snow emissivity.
1658     o pkg/thsice:
1659 jmc 1.809 fix few little problems, in thsice_calc_thickn.F:
1660     - growth vertically (and not laterally) if iceFrac == iceMaskMax
1661 jmc 1.828 - melt only laterally if hIce < hThinIce (as the comments say)
1662 jmc 1.809 and in thsice_extend.F:
1663     - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1664     - start to form ice as soon as the minimum ice-volume is reachable.
1665     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
1666     and cpl_aim+ocn
1667 mlosch 1.807 o pkg/kpp
1668 jmc 1.809 - move computation of surface related input fields to KPP into a new
1669     subroutine kpp_forcing_surf.F
1670 jmc 1.808 - remove wrong (within bi,bj loops) EXCH calls.
1671     - little cleaning (add argument myThid in last position, cvs header ...)
1672 jmc 1.809 - for now, fix conservation problem by exchanging KPPviscAz (may not
1673     be the best fix)
1674 mlosch 1.806 o pkg/seaice
1675     - check for inconsistent evp parameter/cpp-flag combination
1676     - remove leftover errIO flat for obsolete name list error handling
1677 heimbach 1.812 o OpenAD
1678     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1679 mlosch 1.806
1680 jmc 1.1203 checkpoint59a (2007/05/01)
1681 mlosch 1.803 o pkg/seaice: some parameter clarifications and a little bit of clean up
1682 jmc 1.802 o pkg/thsice: rename run-time parameters:
1683     himin -> hIceMin
1684     himin0 -> hThinIce
1685     hihig -> hThickIce
1686     i0 -> i0swFrac
1687     transCoef -> bMeltCoef
1688     frac_energy -> fracMelting
1689     add new parameters: hNewIceMax, fracFreezing, dhSnowLin
1690     with default values (for now) that do not change the results.
1691     remove old version of thsice vars advection in pkg/seaice.
1692 jmc 1.801 o in FFIELDS.h:
1693     - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
1694     - make pLoad & sIceLoad always available (but still only used if
1695     ATMOSPHERIC_LOADING is #define).
1696 dimitri 1.799 o pkg/kpp: replaced _KPP_RL with _RL
1697 dimitri 1.798 o bug fixes for vertical diffusivity computations when both KPP and
1698 dimitri 1.883 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1699     are no longer updating the vertical diffusivity array
1700     (passed as argument) but are (re-) setting those arrays.
1701 mlosch 1.795 o pkg/seaice: fix bug in evp solver, while doing that
1702     - change (improve?) discretization of stress computations for both
1703     cgrid-lsr and evp solver
1704     - add a new routine to compute strain rates
1705 mlosch 1.796 - the above changes lab_sea results
1706     - add no slip conditions for evp solver (off by default), lsr-version
1707     may follow
1708     - fix exchange for shear at Z-points (does not change lab_sea)
1709     - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
1710     (to force the user to pick a time step since there is not "safe" way
1711     of choosing it)
1712 mlosch 1.797 - add principal stress diagnostics
1713 mlosch 1.800 - rearrange fields for evp a little to avoid having to call a: too many
1714     exchanges and b: exchanges for stress trensor components which we do
1715     not have.
1716     - modify Hibler+Bryan (1987) stress coupling so that it reuses information
1717     of evp, complete rewrite for lsr case (latter is does not yet work
1718     in all cases)
1719 mlosch 1.794 o pkg/kpp: add code to have mixing in shelf ice caverns
1720 mlosch 1.804 - add myThid to all kpp routines (long overdue)
1721 mlosch 1.794
1722 jmc 1.1203 checkpoint59 (2007/04/19)
1723 heimbach 1.792 o pkg/exf:
1724     - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
1725     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
1726     - move exf header files from lower_case.h to UPPER_CASE.h ;
1727     add missing cvs Header & Name
1728     - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
1729 heimbach 1.793 - add namelist param. selectStressGridPosition, exf_monFreq
1730     - retire many _CLIM routines, and remove data.exf_clim
1731     + params moved to data.exf
1732     + climsst, climsss now handled by exf_set_gen, i.e.
1733     climss?period=0 refers to constant field,
1734     climss?period=-12 to monthly forcing
1735     - split up namelists in data.exf
1736 mlosch 1.788 o pkg/seaice:
1737     - remove seaice_exch and seaice_exch_uv
1738     - remove superfluous exchange of theta
1739     - add myThid to seaice_budget_ocean/ice
1740 mlosch 1.790 - add new interface for atmospheric wind forcing (C-grid only)
1741     + new routine
1742     + two new field (taux, tauy for stress over ice)
1743     + removed one global field (DAIRN) for C-grid case only
1744 heimbach 1.792 o pkg/thsise
1745     - 2nd set of modifs for thsice adjoint in conjunction with exf
1746 heimbach 1.793 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
1747 mlosch 1.788
1748 jmc 1.1203 checkpoint58y_post (2007/04/15)
1749 dimitri 1.785 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
1750 dimitri 1.786 vertical diffusivity, similar to that in MOM4; turned on using
1751     #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
1752     diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
1753 dimitri 1.782 o Added capability for 3D specification of background vertical diffusion
1754     coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
1755     in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
1756     "data" file that contains the 3D vertical diffusivity coefficients.
1757 jmc 1.784 o ice dynamics (pkg/seaice) with thsice thermodynamics:
1758     - add code within pkg thsice to advect & diffuse sea-ice fields
1759     similar to (and will replace) what has been added in seaice_advdiff.F,
1760     but: - conserving Mass, Heat & Salt.
1761     - better when using non-linear advection scheme (not yet fully tested)
1762     - can also be used in atmospheric set-up (for now, only the diffusion).
1763 dimitri 1.783
1764 jmc 1.1203 checkpoint58x_post (2007/04/04)
1765 jmc 1.779 o IO option for global-file compact format:
1766     - add options when generating topology (utils/exch2/matlab-topology-generator)
1767     - add I/O capability (pkg/mdsio).
1768     - adapt utils/matlab/rdmds.m to read this format.
1769     for now long-line format not yet supported by pkg/mdsio (& exch2).
1770 mlosch 1.778 o shelfice: add a few diagnostics
1771    
1772 jmc 1.1203 checkpoint58w_post (2007/03/13)
1773 jmc 1.776 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
1774     rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
1775     (and replace horiVertRatio in NH code).
1776     Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
1777     and tutorial_plume_on_slope (sensitive to truncation)
1778 mlosch 1.774 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
1779     directly to drive seaice model (C-grid only)
1780     o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
1781     - reintroduce computation of wind from stress,
1782     - compute tau (in exf_bulkformulae.F) from windstress averaged to
1783     mass points to avoid tau = 0
1784 mlosch 1.775 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
1785 mlosch 1.774 o rdmnc.m: make it work with "global" files created with gluemnc
1786 jmc 1.773 o rdmnc.m : some improvements in dealing with singleton dimension
1787     (tested on all testreport mnc output files).
1788     o genmake2: disable pkg/profiles if netcdf test fails.
1789 jmc 1.772 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
1790 mlosch 1.771 o move call to cal_readparms up to make calendar parameters/variable available
1791     to all packages
1792    
1793 jmc 1.1203 checkpoint58v_post (2007/02/08)
1794 jmc 1.770 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
1795     useDynP_inEos_Zc tested.
1796 dimitri 1.769 o pkg/exf: changes to properly interpolate/mask/scale initial fields
1797 dimitri 1.768 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1798     and portions thereof. See read_cs.txt for description and examples.
1799 jmc 1.767 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1800     add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1801     following the great-circle arc between those 2 points.
1802     o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1803     (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1804 jmc 1.766 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1805     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1806     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1807     - still needs work (not working with some options ; efficiency to improve)
1808     and serious testing.
1809     - use this scheme for temperature & salinity in 2 advection test exp.:
1810     advect_xy & advect_xz, respectively.
1811    
1812 jmc 1.1203 checkpoint58u_post (2007/01/12)
1813 jmc 1.765 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1814 jmc 1.764 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1815     o testreport: add option "-skipdir" to skip some test.
1816     o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1817     momentum calculation.
1818     o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1819     o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1820     remove checkpoint.F and the_correction_step.F (no longer used);
1821     do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1822     o add option (linFSConserveTr) to correct for tracer source/sink due to
1823     Linear Free surface
1824 mlosch 1.763 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1825     o pkg/thsice: fix reading mnc-pickups
1826    
1827 jmc 1.1203 checkpoint58t_post (2006/12/30)
1828 jmc 1.761 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1829     o pkg/mdsio:
1830     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1831     move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1832     mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1833     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1834     - collect old S/R in one file: mdsio_rw_field.F (now just a call to
1835     either MDS_READ_FIELD or MDS_WRITE_FIELD )
1836     - new S/R (to replace MDSWRITEMETA), which allows to write more
1837     informations (variable names, time ...) to meta files.
1838     - modify rdmds.m to give back the meta file content.
1839 jmc 1.760 o pkg/diagnostics: change vertical interpolation to be safer, and more
1840     flexible (define p-levels to interpolate to in data.diagnostics);
1841     add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1842     diagnostic pointer.
1843 mlosch 1.759 o pkg/seaice: more cleaning up of seaice_growth, added many comments
1844 mlosch 1.763 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1845 mlosch 1.757 o fix multi-category seaice:
1846     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1847     SEAICE_MULTICATEGORY
1848     - fix short wave heat flux
1849 jmc 1.758 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1850     and allow to use EVP solver. Change forward lab_sea: test both EVP
1851     solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1852 heimbach 1.756 o Initial check-in of lab_sea adjoint
1853     (very similar to natl_box_adjoint/code_seaice)
1854     * used C-grid and EVP solver
1855     * used KPP, GM/Redi
1856     * uses inAdExact=.TRUE.
1857     * gradient checks fail for both ADM and TLM
1858     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1859     f.d. gradients actually seem more problematic than ADM, TLM gradients;
1860     issue is related to forward mismatch between g77 an ifort
1861 mlosch 1.755 o pkg/seaice: overhaul of thermodynamics
1862     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1863     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1864     - move a few global fields out of SEAICE.h into seaice_growth.F and
1865     make them 2D (FICE/QNETO/ ...)
1866     - remove FO (it is the same as QNETO)
1867     - introduce a few local fields to avoid modifying external fields such
1868     as atemp, etc.
1869    
1870 jmc 1.1203 checkpoint58s_post (2006/12/11)
1871 dimitri 1.753 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1872     changed exf_set_gen.F so that
1873     genperiod=0 means input file is one time-constant field and
1874     genperiod=-12 means input file contains 12 monthly means
1875 jmc 1.752 o CG2D: use pre-computed solver main-diagonal (stored in common block);
1876     this affects truncation error ; generate new output file for exp. which
1877     fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1878     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1879     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1880     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1881     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1882     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1883 jmc 1.751 o start implementation of deep-atmosphere and anelastic formulation
1884 jmc 1.750 o verification: remove 2nd copy of input files and use script "prepare_run"
1885     to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1886 mlosch 1.749 o mom_common/vecinv/fluxform: fix a few initialisation isssues
1887 gforget 1.748 o profiles: fix for multithreaded case
1888    
1889 jmc 1.746 o diagnostics: rename few diags:
1890     s/'PRESSURE'/'RCENTER '/g
1891     s/'TICE '/'oceFreez'/g
1892     s/'TAUX '/'oceTAUX '/g
1893     s/'TAUY '/'oceTAUY '/g
1894     s/'SWFLUX '/'oceQsw '/g
1895     s/DIFx/DFxE/g
1896     s/DIFy/DFyE/g
1897     and add few ocean-forcing diagnostics:
1898     atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1899 dimitri 1.747 o modifications to pkg/seaice/growth.F and budget.F, which change results of
1900     lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1901     as actual snow thickness. It now refers everywhere to effective snow
1902     thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1903 jmc 1.746
1904 jmc 1.1203 checkpoint58r_post (2006/11/17)
1905 dimitri 1.744 o modifications to pkg/seaice/growth.F, which change results of
1906     lab_sea experiment: fixes pertain to melting snow over open water, to
1907     masking EVAP under sea ice, and to using the correct AREA variable for
1908     computations of EVAP, PRECIP, HSNOW, and GHEFF
1909 edhill 1.743 o add ability to read bathy, salt, and theta using MNC (off by def)
1910 mlosch 1.742 o add flooding algorithm and advection of HSNOW for pkg/seaice;
1911     both are turned off by default and do no change any results
1912 jmc 1.741 o seaice advection with pkg/thsice: a step toward the use of non-linear
1913     advection scheme, but #ifdef or commented out for now (requires more EXCH).
1914 jmc 1.739 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1915     (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1916     in natl_box (affects results @ truncation level: update output.txt)
1917     o multi-threading and IO:
1918 jmc 1.738 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1919     - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1920     (needed to work with SingleCpuIO): tested in all verif. exp.
1921 jmc 1.737 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1922     affects the results (but none of the verification test uses this scheme).
1923 heimbach 1.736 o Adding some pkg/diagnostics capability to pkg/seaice
1924     (will certainly be subject to changes)
1925 heimbach 1.740 o ctrl: adding new control variables:
1926     lwflux, lwdown, evap, snowprecip, apressure, runoff
1927 heimbach 1.736
1928 jmc 1.1203 checkpoint58q_post (2006/10/20)
1929 dimitri 1.734 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
1930     1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1931     high_res_cube configuration by 4% on Columbia.
1932 jmc 1.733 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1933     add (in global_with_exf/code) a version of EXF_INTERP_READ without
1934     dynamical allocation (seems to work in multi-threaded).
1935     o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1936     single CPU io) so that TAF does not have to see EESUPPORT.h
1937 jmc 1.727 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1938    
1939 jmc 1.1203 checkpoint58p_post (2006/09/08)
1940 mlosch 1.726 o obcs: stop if obcs is used with useCDscheme = .true.
1941 mlosch 1.723 o shelfice:
1942     - fix a sign error so that no slip at shelfice interface works
1943     - remove stop for combination non-hydrostatic code and shelfice. That does
1944     not mean, that the results are correct, but at least they are numerically
1945     stable
1946 dfer 1.721 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1947 heimbach 1.724 o added adjoint exch routined for all exch*3d* routines
1948     and updated flow directives
1949 dfer 1.721
1950 jmc 1.1203 checkpoint58o_post (2006/08/28)
1951 jmc 1.720 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1952     remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1953 jmc 1.719 o change controling S/R for writing pickup file (new S/R do_write_pickup)
1954     and clean-up reading/writing of pickup files.
1955     o fix local version of read/write pickup (NH part) in rotating_tank/code
1956 jmc 1.718 o simplify EXCH interface:
1957     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1958     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1959 edhill 1.717 o added the regrid package
1960 mlosch 1.716 o shelfice:
1961     - add a simple boundary layer scheme to reduce noise
1962     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1963 jmc 1.718
1964 jmc 1.1203 checkpoint58n_post (2006/08/14)
1965 jmc 1.713 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1966     local variable (not in common block).
1967 jmc 1.712 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1968     - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1969     - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1970     to work with SingleCpuIO.
1971 jmc 1.711 o add "_d 0" to real constant of pkg/cfc subroutines ;
1972     update exp. cfc_exemple & tutorial_cfc_offline output files.
1973 jmc 1.710 o multi-threading and IO:
1974     - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1975     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1976     - barrier before and after reading.
1977     - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1978     - avoid using MDS_WRITELOCAL for LAND pkg output.
1979     - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1980     common-block variables ; Allows multi-threading with master-thread IO.
1981 jmc 1.709 o change default MAX_NO_THREADS from 32 to 4 ;
1982     and stop cleanly when MAX_NO_THREADS is too small.
1983     o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1984    
1985 jmc 1.1203 checkpoint58m_post (2006/07/17)
1986 jmc 1.707 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1987     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1988 jmc 1.706 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1989     keep global_ocean.90x40x15 (for AD testing) with former secondary test
1990     (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1991     o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1992     add MITgcm_tutorials (= code + all the tutorials)
1993 gforget 1.705 o ecco, option to compute cost for total ssh (mean+anom)
1994 gforget 1.704 o consistent with addition of ptracer and ssh in pkg/profiles
1995 gforget 1.703 o profiles: adding ptracer and ssh
1996 jmc 1.702 o testreport: change multi-test output-file name
1997     (from output.txt.{name} to output.{name}.txt)
1998 jmc 1.712 o profiles: now ok for mutli-tiles case
1999 mlosch 1.700 o seaice: add 4 parameters for different advection schemes for area,
2000     (effective) seaice thickness, enthalphy, and snow height. Their default
2001     is the standard parameter SEAICEadvScheme
2002 jmc 1.699 o calc_gw:
2003     - add cosFacU in zonal viscous flux (harmonic.visc.).
2004     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
2005     of tutorial_plume_on_slope.
2006     o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
2007 jmc 1.698 o calc_gw: true flux-form, account for horizontal grid spacing.
2008     update rotating_tank results, but not plume_on_slope (affected at
2009     truncation level, 11 digits).
2010    
2011 jmc 1.1203 checkpoint58l_post (2006/07/12)
2012 jmc 1.698 o calc_gw:
2013     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
2014     - remove side-drag for now (need to fix it); update plume_on_slope results.
2015     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
2016 heimbach 1.695 o commit code to make SST/SSS weights spatially variable
2017     (based on either variable in-situ or variable initial T/S weights)
2018 heimbach 1.696 o pkg/ecco:
2019     * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
2020     now based on horizontally varying weights wthetaLev, wsaltLev
2021     * cost_averagesflags now returns year indices in addition to day, month
2022     * sflux balance is performed on annual basis
2023     (sflxumm, sfluxmm2, bal_sfluxmm)
2024     * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
2025     including separate counting and multipliers
2026 heimbach 1.697 o pkg/rbcs
2027     * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
2028 jmc 1.694
2029 jmc 1.1203 checkpoint58k_post (2006/07/06)
2030 jmc 1.692 o testreport:
2031     - always build in dir. "build" (if not there, mkdir build instead of building
2032     & running in input)
2033     - run in dir run (if it exists), in build otherwise.
2034     - call prepare_run (if input/prepare_run exists)
2035     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
2036 dimitri 1.691 o pkg/exf modifications to interpolation and rotation routines for more
2037     reasonable treatment of North Pole singularity: for tracers North Pole
2038     value is set to northernmost zonal-mean value, for zonal velocity it is
2039     set to zero, and for meridional velocity it is set to northernmost value.
2040 mlosch 1.690 o pkg/exf/exf_check_range.F
2041     - add tile index to diagnostics and move stop statement to the very
2042     end of the routine.
2043 jmc 1.689 o pkg/diagnostics: (diagnostics_main_init.F)
2044     define title of isomorphic variables according to the current config.
2045 jmc 1.687 o pkg/thsice with pkg/seaice dynamics:
2046 jmc 1.688 - fix domain of computation (interior only, required for exf) and do exchanges
2047     - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
2048 jmc 1.686 o towards a standard way of dealing with multi-threading in MONITOR
2049     and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
2050 baylor 1.685 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
2051     to W momentum equation in nonhydrostatic and quasihydrostatic runs.
2052 jmc 1.684 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
2053 jmc 1.683 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
2054     o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
2055     (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
2056 jmc 1.682 o tracer advection:
2057     - clean-up and simplify calc_common_factors.F
2058     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
2059     advection subroutine (but still not used within DST advection S/R)
2060 jmc 1.681 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
2061    
2062 jmc 1.1203 checkpoint58j_post (2006/06/15)
2063 heimbach 1.680 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
2064     from file (collects calls previously in FORWARD_STEP)
2065     o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
2066 heimbach 1.679 o adjoint store dir. adjusted accordingly
2067 heimbach 1.680 o genmake2
2068     replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
2069 heimbach 1.679
2070 jmc 1.1203 checkpoint58i_post (2006/06/14)
2071 mlosch 1.677 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
2072     on wind stress (SEAICEstressFactor defaults to 1.)
2073 jmc 1.676 o Total number of Timers is finite (<=40): comment out 2 non-essential one
2074     in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
2075 jmc 1.675 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
2076     on CS-grid: no longer loosing mass.
2077 jmc 1.674 o exf & curvilinear-grid: no longer modify longitude xC & xG.
2078 mlosch 1.670 o pkg/ggl90: fix sloppy output and fix a bug
2079 dimitri 1.672 o pkg/seaice: added SEAICEuseEVPpickup parameter
2080     - Set to false in order to start EVP solver with
2081     non-EVP pickup files when using SEAICEuseEVP
2082 mlosch 1.673 - fix sign error in diffusion in seaice_calc_rhs
2083 mlosch 1.670
2084 jmc 1.1203 checkpoint58h_post (2006/06/07)
2085 heimbach 1.669 * Modifications for bottom topography control
2086     o replace hFacC by _hFacC at various places
2087     o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
2088     o add non-self-adjoint cg2d_nsa
2089     o update autodiff support routines
2090     o re-initialise hfac after ctrl_depth_ini
2091     o works for 5x5 box, doesnt work for global_ocean.90x40x15
2092     * Adding verification for 5x5 box (4-layer) bottom topography control
2093    
2094 jmc 1.1203 checkpoint58g_post (2006/06/07)
2095 jmc 1.671 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
2096     used for mean seasonal cycle, mean diurnal cycle); add an example
2097     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
2098 mlosch 1.667 o pkg/ggl90:
2099     - add parameter (minimum surface kinetic energy)
2100     - fix bug (avoiding division by zero)
2101 mlosch 1.665 o couple pkg/thsice to pkg/seaice:
2102     - modify advection in seaice to accomodate new scalar fields to be advected
2103     - only muliDimAdection scheme work with seaice/thsice
2104     - mapping of thsice-variables to seaice-variables, back and forth
2105     - does not break the verification experiments, but does not give the
2106     desired results either
2107     o pkg/seaice
2108     - make (default) second order advection a bit less confusing?
2109    
2110 jmc 1.1203 checkpoint58f_post (2006/06/05)
2111 mlosch 1.662 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
2112     to pkg/seaice):
2113     - new routines thsice_map_exf and thsice_get_exf provide the interface
2114     - add an additional formal parameter to thsice_solve4temp
2115 heimbach 1.661 o pkg/exf:
2116     - add new fields wspeed, snowprecip (to be able to couple to thsice)
2117     - correct Stefan-Boltzmann constant
2118     - new parameter for longwave surface emittance
2119     - separate some stuff from exf_bulkformulae into new routines
2120     exf_radiation, exf_wind
2121 mlosch 1.662 - add new parameters and constants: longwave emissivity for ocean, ice
2122     and snow, evaporation parameters over ice
2123 mlosch 1.663 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
2124     either wind from stress or stress from wind
2125 jmc 1.660 o pkg/thSIce:
2126     - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
2127     - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
2128     and THSICE_CALC_THICKN
2129     - for now, call to THSICE_GET_BULKF remains inside i,j loops.
2130     - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
2131     to make debugging easier.
2132     - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
2133     o pkg/bulk_force:
2134     - clean-up comments and parameters ;
2135     - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
2136 jmc 1.659 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
2137     generate new output for test-experiment: aim.5l_cs.thSI
2138 jmc 1.658 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
2139 heimbach 1.661 testreport accordingly
2140 jmc 1.658
2141 jmc 1.1203 checkpoint58e_post (2006/05/17)
2142 heimbach 1.656 o SEAICE_CGRID adjoint done
2143 heimbach 1.654 o R_STAR adjoint implemented.
2144     * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
2145     * need to sort out init. of h0facc, etc.
2146 heimbach 1.655 o Make pkg/profile fully independent of ecco,cost, etc. stuff
2147     to be able to use it in pure forward.
2148 heimbach 1.653
2149 jmc 1.1203 checkpoint58d_post (2006/04/21)
2150 jmc 1.651 o upgrade simple test-experiment to tutorial example:
2151     step.1: duplicate the experiment and (step.2) will remove the old copy.
2152     tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
2153     tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
2154     tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
2155     tutorial_global_oce_biogeo <- copy of dic_example
2156     tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
2157     tutorial_plume_on_slope <- copy of plume_on_slope
2158     tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
2159     tutorial_global_oce_optim <- empty for now (David ?)
2160     tutorial_global_oce_in_p <- copy of global_ocean_pressure
2161     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
2162 gforget 1.650 o correct a sign problem in cost_scat.F
2163 mlosch 1.649 o obcs and ptracers: fix boundary conditions for advections schemes
2164     with larger stencil
2165 heimbach 1.648 o thsice adjoint: start
2166 mlosch 1.647 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
2167     completeness
2168 mlosch 1.646 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
2169     and COSINEMETH_III, add comments in default CPP_OPTIONS.h
2170 heimbach 1.645 o ptracers adjoint:
2171     * avoid extensive recomputatations
2172     * fix missing re-init. of gptr (missed by TAF)
2173 mlosch 1.644 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
2174     me to turn off the excessive output to STDOUT that this package produces
2175 jmc 1.643 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
2176     and add those terms in Vector-Invariant formulation.
2177 gforget 1.642 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
2178     if the control period (xx_hfluxperiod etc) is 0
2179     o in profiles pkg, clean routines and fix details
2180     o in ecco pkg, reading ssh data:
2181     fix problem in case the model does not start at iter0=0
2182 mlosch 1.640 o fix mnc-pickup/restart for ptracers
2183 heimbach 1.641 o new package prifiles:
2184     code to compute profile-based cost by Gael Forget
2185 heimbach 1.639 (modifs in ecco, ctrl, autodiff)
2186 heimbach 1.641 o Benign bug fix in initialization (spotted by M. Mazloff) of
2187     ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
2188 heimbach 1.639
2189 jmc 1.1203 checkpoint58c_post (2006/03/23)
2190 heimbach 1.638 o adjoint: finish NLFS adjoint and provide reference output in
2191     verification/global_ocean.90x40x15/results_ad_nlfs
2192 mlosch 1.637 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
2193     documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
2194     SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
2195     with SEAICE_CGRID defined.
2196 jmc 1.636 o move calendarDumps from "data" to "data.cal" and clean-up the code
2197     with a simple call to pkg/cal S/R: CAL_TIME2WRITE
2198     o add useEXF & useCAL flags (for now, set in hard-coded way)
2199 jmc 1.635 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
2200     (were missing in NH mode, and wrong in quasihydrostatic mode).
2201     waiting for Chris updated version of calc_gw to add those CALLs.
2202     o fix bug in quasihydrostatic S/R ;
2203     add a test for this option: global_ocean.90x40x15.qshyd
2204 jmc 1.634 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
2205     (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
2206     o add on/off flag useOffLine for package OFFLINE
2207 mlosch 1.630 o seaice:
2208     - modify advection so that it works also on the C-grid
2209     - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
2210     problem in multi-tile runs with C-grid
2211 mlosch 1.633 - add flags for clipping ice velocities and/or masking solver forcing
2212 mlosch 1.631 - fix drag (ocean on ice) formulation and a bug that caused noise in the
2213     C-grid solver
2214 mlosch 1.632 - added a few comments to seaice_diffusion.F
2215     - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
2216     are now exclusive)
2217     - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
2218     required re-ordering the code a little:
2219     + make DAIRN global variable (defined in SEAICE)
2220     + move computation of the viscosities eta and zeta into a new separate
2221     routine (because I need to recompute them in seaice_ocean_stress.F)
2222 mlosch 1.629
2223 jmc 1.1203 checkpoint58b_post (2006/03/13)
2224 jmc 1.627 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
2225     update output.txt of exp. aim.5l_cs.thSI
2226 edhill 1.626 o various mnc cleanups and improvements:
2227     + shrink lookup tables by factor of ~4
2228     + better error reporting when running out of lookup space
2229     + able to handle longer path/file names (up to 500 chars)
2230 heimbach 1.625 o adjoint:
2231     - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
2232     - TBD: "hidden" mom_vecinv recomp. in dynamics
2233 jmc 1.624 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
2234     (allow to differentiate between forcing components using new integer flags:
2235     momForcingOutAB=1/0 & tracForcingOutAB=1/0)
2236     and add new flag to put Dissipation tendency out of Adams-Bashforth.
2237 heimbach 1.623 o ecco
2238     - enable trend removal from SSH anomaly obs.
2239     o adjoint
2240     - a fix for PmEpR when #undef EXACT_CONSERV
2241     - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
2242     - try to fix "hidden" recomp. in forward_step for NLFS
2243     (NLFS seems broken sometimes after I checked it in)
2244 mlosch 1.622 o seaice:
2245     - add c-grid version of the dynamic solver:
2246     + three new routines that are the c-grid substitute lsr, dynsolver
2247     and ostres
2248     + put a few fields that were local to dynsolver into global common
2249     blocks, so that I can move the computation of stresses etc into
2250     seaice_lsr (saves coding but may break the adjoint).
2251     - replace more hardwired parameters by runtime parameters
2252     - add ice masks that mask the rhs of the implicit solvers where there
2253     is no ice (commented out in seaice_dynsolver, because i am not sure
2254     if this works properly), eventually this should replace the clipping
2255     of ice velocities in seaice_dynsolver to +/-40cm/s.
2256 edhill 1.621 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
2257     include it only where its needed
2258 mlosch 1.620 o move balancing of fluxes before the call of external_forcing_surf
2259 mlosch 1.619 o seaice:
2260     - correct units of turning angles (now they are really in degrees)
2261     - move computation of GWATX/Y out of main routine into dynsolver
2262     - initialize GWATX/Y in seaice_init
2263 jmc 1.618 o Apply mask on Fresh-Water flux (needed for SSH forcing).
2264 mlosch 1.619 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
2265 mlosch 1.617 o seaice: add runtime flags for turning angles (default to zero)
2266 heimbach 1.616 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
2267     and trend from exf forcing and ctrl control adjustments
2268     o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
2269     (since checkpoint57x_post)
2270 jmc 1.615 o change the default rotation period to 86164.s = the Earth rotation
2271 jmc 1.614 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
2272     and based on a reference stratification. Tested within hs94.cs-32x32x5.
2273 mlosch 1.613 o seaice advection: add code for choosing between the default (2nd order
2274     central differences) and multiDim advection schemes provided by
2275     pkg/generic_advdiff
2276 mlosch 1.611 o seaice:
2277     - removed all references to SEAICE_GRID.h fields from
2278     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
2279     (cubed-sphere configuration will change a little)
2280     - grid computations in seaice_init are obsolete now.
2281     - cleaned up code a little so that is easier to read (hopefully).
2282 mlosch 1.613 - added new (better?) discretizations of default advection and diffusion
2283     (turn on with SEAICEuseFluxForm)
2284     - replace 1 in 3d global fields by kSurface in growth.F
2285 mlosch 1.611
2286 jmc 1.1203 checkpoint58a_post (2006/02/13)
2287 mlosch 1.612 o seaice:
2288     - bug fix in advect.F
2289 mlosch 1.608 o shelfice:
2290     - separate shelfice load anomaly from pload (breaks with time
2291     dependent forcing), => introduce constant field shelficeLoadAnomaly.
2292     Its default is 0., but it may be computed more cleverly from (unknown)
2293     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
2294     done offline. A good approximation of the pressure load anomaly is
2295     necessary to avoid large initial adjustment processes underneath
2296     deep-reaching shelfice.
2297 mlosch 1.609 - small fix in ISOMIP shelfice_thermodynamics
2298     - add more sophisticated thermodynamics of Hellmer (1989), this is
2299     now the default
2300     - give a few constants more intuitive names
2301 mlosch 1.607 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
2302     if bulk formulae are used in long integration (especially EmPmR). Turn
2303     on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
2304     if balancePrintMean, the imbalance that is substracted is printed to
2305     STDOUT.
2306 jmc 1.606 o fix bug (typo) in obcs_apply_eta.F
2307 mlosch 1.605 o add a new package shelfice which enables us to model the circulation
2308     underneath shelf-ice with draughts of hundreds of meters.
2309     - works
2310     - to do: + include improved thermodynamics
2311     + check whether kSurfC (from model/inc/SURFACE.h) can be used
2312     instead of new field kTopC
2313     + can we use topoFile, Ro_surf and existing code in ini_depth.F
2314     instead of new field R_shelfIce and new code in ini_depth.F
2315     and ini_mask_etc.F?
2316 mlosch 1.608 + adjust vertical mixing schemes?
2317 mlosch 1.604 o seaice pkg:
2318     - add a cpp-flag to include a simple formula for a salinity dependent
2319     freezing point of sea water at the surface
2320     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
2321     meridional stresses are now different (and hopefully correct)
2322 jmc 1.602 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
2323     update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
2324     and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
2325 jmc 1.601 o pkg/diagnostics: add options and parameters for regional-statistics
2326     diagnostics ; define regions by reading a region-mask from a file
2327     (might add other options later)
2328 jmc 1.600 o pkg/bulk_force:
2329     - add option and parameters to use AIM surface-flux formulae.
2330     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
2331     others forcing fields (defined in PARM05, parameter file "data") are loaded
2332     from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
2333     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
2334     - use the right EXCH call for uwind,vwind (to work on CS-grid).
2335     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
2336     and parameters (note: calcWindStress replaces .NOT.readwindstress).
2337     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
2338    
2339 jmc 1.1203 checkpoint58 (2006/01/12)
2340 edhill 1.598 o add "--embed-source" option to genmake2 which, when the supporting
2341     tools can be compiled (as determined by genmake2) will turn on the
2342     embed_files package which then embeds the entire MITgcm source code
2343     (*.[fFhc] + Makefile) used for the build within the executable
2344     - requested by CNH but off by default
2345     - adds a paltry <9MB to the mitgcmuv executable in most cases
2346     - only writes the output when useEMBEDSRC in eedata is true
2347 heimbach 1.597 o clean up 3-dim. relaxation codes:
2348     * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
2349     * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
2350     * Thanks to Tom Haine for testing!
2351    
2352 jmc 1.1203 checkpoint57z_post (2005/12/31)
2353 jmc 1.593 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
2354     affects output (@ truncation level) of exp. plume_on_slope ; updated.
2355 mlosch 1.592 o fix the pickup behavior for obcs in combination with ptracers
2356     o fix a bug in ptracers_external_fields_load
2357     o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
2358     affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
2359     o transfered surface NH pressure to eta field (if exactConserv).
2360 jmc 1.589 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
2361     and update lab_sea output.txt file.
2362 heimbach 1.590 o completing 3-dim. relaxation code: additional term
2363     1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
2364     in S/R EXTERNAL_FORCING_T (file external_forcing.F)
2365     * At compile time, in "EXF_OPTIONS.h" set
2366     #define ALLOW_CLIMTEMP_RELAXATION
2367     #define ALLOW_CLIMSALT_RELAXATION
2368     * At runtime in "data", under &PARM03 set (e.g., units in seconds)
2369     tauThetaClimRelax3Dim = 15552000.0,
2370     tauSaltClimRelax3Dim = 15552000.0,
2371     * 3 cases:
2372     1) Use a constant-in-time 3-dim. field
2373     2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
2374     3) Real-time relax. to time-evolving prescribed field
2375 heimbach 1.595 o Adding Laplacian-type smoothness constraint on
2376     initial and boundary (forcing) controls (ic, bc)
2377     * enable at compile-time via
2378     ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
2379     * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
2380 heimbach 1.594 * Absolute scale somewhat unclear so far
2381     * no area weighting was included since no other cost term does so far
2382 jmc 1.589
2383 jmc 1.1203 checkpoint57y_post (2005/12/08)
2384 heimbach 1.588 First step for a NLFS adjoint
2385     o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
2386     o new init. routines for calc_r_star, calc_surf_dr
2387     o still need to deal with ini_masks_etc
2388     o testreport seemed happy
2389 jmc 1.1203 checkpoint57y_pre (2005/12/08)
2390 heimbach 1.587
2391 jmc 1.586 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
2392 stephd 1.585 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
2393 stephd 1.584 o add new offset feature to offline pkg (plus minor cleanup)
2394     o cfc fixes for final year of integration
2395     o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
2396     be in GCHEM_OPTIONS).
2397    
2398 jmc 1.1203 checkpoint57x_post (2005/12/04)
2399 jmc 1.583 o fix testreport Pb in multiple test experiment.
2400 edhill 1.582 o cleanup our namelist syntax in verification:
2401     - make it more F95 standards compliant (some work still needed)
2402     - allows the vast majority of our tests to work with gfortran
2403 jmc 1.580 o Non-Hydrostatic:
2404     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
2405     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
2406 jmc 1.579 o Allow to apply AB on T,S rather than on AB(gT,gS):
2407     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
2408     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
2409     time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
2410     - need a "clever" read_pickup to restart from the other AB formulation
2411 jmc 1.578 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
2412     o remove some unused variables (reduces number of compiler warnings)
2413 heimbach 1.581 o adjoint
2414     * Disable useVariableViscosity for adjoint for time being
2415     (there are a number of extensive recomputations)
2416     * Initialize certain variables needed for adjoint
2417 jmc 1.578
2418 jmc 1.1203 checkpoint57w_post (2005/11/03)
2419 jmc 1.576 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
2420     fix the singleCpuIO RS version of MDSWRITEFIELD
2421     and add a WARNING if using globalFiles=T with multi-processors.
2422 jmc 1.575 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
2423     using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
2424 jmc 1.576 o tracer advection scheme:
2425 jmc 1.574 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
2426     those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
2427     was not very convenient).
2428     add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
2429     (further tests needed for the implicit DST & Flux-Limiter schemes).
2430 mlosch 1.573 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
2431     and sRef for convenience, handy, when you want to initialize
2432     ptracers in a large domain with a constant non-zero value. Also,
2433     untangle ptracers_init.F a little.
2434    
2435 jmc 1.1203 checkpoint57v_post (2005/10/13)
2436 jmc 1.572 o change dome exp. to use variable viscosity in side-drag terms.
2437 edhill 1.570 o remove all the files from the cfc_offline test since they are now
2438     incorporated into tutorial_cfc_offline which has been producing
2439     identical results for a few days of testing
2440 jmc 1.571 o add new parameter: sideDragFactor to enable half-slip-side BC
2441     and change side-drag S/R to use viscosity from mom_calc_visc
2442     (can switch back by setting sideDragFactor=0.); affects results at
2443     truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
2444     global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
2445 jmc 1.569 o vorticity & strain are now computed without masking, to account for
2446     no-slip-side BC in variable viscosity calculation ; mask is applied
2447     anyway later on, before computing advection/coriolis terms.
2448 mlosch 1.573 o modify exp4 to test new obcs support for reading from external files
2449 mlosch 1.568 and for passive tracers
2450 mlosch 1.567 o fix behavior of ptracers_monitor when monitor output is written to a
2451     netcdf-file; still not independent of monitor.F (writes in the same
2452     file).
2453 jmc 1.566 o change default value of tRef (put a uniform, meaningful value for ocean
2454     & atmos) and initialize sRef (was missing, as Martin mentioned).
2455 baylor 1.565 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
2456     to be proportional to enstrophy dissipation length. Thus,
2457     viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
2458     This is now consistent with Smagorinsky and with the manual.
2459    
2460 mlosch 1.564 checkpoint57u_post
2461 mlosch 1.562 o OBCS and PTRACERS: add open boundary support for passive tracers
2462     - either use homogenous (pseudo) v.Neumann conditions or prescribe
2463     OB-values from file; this is not different from the way theta and salinity
2464     are treated
2465     - however, Orlanski-radiation conditions are not supported, and the model
2466     will stop if you use pTracers and Orlanski at the same time.
2467     - beefed up the rountine obcs_external_fields_load: now only those open
2468     boundary values are overwritten with values from files for which there
2469     are really files, otherwise the OB-fields remain untouched. This makes
2470     it possible to use different OBs at different ends of the domain (as
2471     with EXF)
2472 jmc 1.561 o reduce number of exch calls in shap_filt (s2).
2473 jmc 1.560 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
2474     truncation level) 4/5 MLAdjust test results (11&12 digits match).
2475    
2476 jmc 1.1203 checkpoint57t_post (2005/10/03)
2477 jmc 1.558 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
2478     o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
2479     same truncation, independent of the face number: affects affects several
2480     test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
2481 jmc 1.557 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
2482 jmc 1.558 note that biharmonic viscosity + no-slip was not tested in any experiment.
2483 jmc 1.556 o fix bug in non-linear free-surf side-drag ; generate new output for
2484     global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
2485 edhill 1.555 o make mnc honor the writeBinaryPrec flag for most kinds of output
2486 edhill 1.554 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
2487 jmc 1.553 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
2488     error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
2489 jmc 1.552 o add brackets in multi-terms sum to get same truncation, independent of
2490     the face number (manage to get exactly same value of gU,gV at the cs-edge)
2491     affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
2492 baylor 1.551 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
2493     and viscA4Remax, which allow one to limit the minimum viscosity by specifying
2494     a maximum grid-scale Reynolds number. Also, changes all length calculations
2495     in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
2496     Suggested values of viscosity parameters found in mom_calc_visc.
2497     Many new viscosity diagnostics available.
2498 jmc 1.550
2499 jmc 1.1203 checkpoint57s_post (2005/09/20)
2500 baylor 1.549 o Add clearing-house for viscosity calculations, mom_calc_visc and
2501     correct numerous bugs in LeithD and Smagorinsky discretizations.
2502     mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
2503     used simultaneously, and to be used in mom_vecinv and mom_fluxform.
2504     Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
2505     and with Strain-Tension viscous term calculation (mom_hdissip.F).
2506     The Strain-Tension form is now called with useStrainTensonVisc=.true.
2507     ViscAhStrain and viscAhTension are now retired.
2508 jmc 1.550 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
2509 edhill 1.547 o In response to JMC's bug report, genmake2 now ignores any soft-links
2510     that it finds in the *current* directory when searching for files.
2511     Soft-links found in any other source directories will still work as
2512     they did before.
2513 edhill 1.546 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
2514     a C routine to unlimit the stack size
2515 edhill 1.545 o mnc-ify pkg/aim snapshot vars
2516 edhill 1.544 o mnc-ify pkg/land as requested by Daniel
2517 edhill 1.543 o various changes to mnc including:
2518     - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
2519     - output can now be grouped so that all files within a group
2520     change the ITER portion of their names in lock-step together
2521     - can now read ("global") PER-FACE (in addition to PER-TILE) files
2522     and works with both EXCH1 and EXCH2 (but needs more testing)
2523     - writing works for all verification test cases w/ g77 on Linux
2524    
2525 jmc 1.1203 checkpoint57r_post (2005/09/07)
2526 edhill 1.541 o make MNC variable initialization happen earlier
2527 jmc 1.540 o add diagnostics for (almost) each term of the momentum Eq.
2528 jmc 1.537 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
2529 jmc 1.536 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
2530     o remove MINIMAL_TAVE_OUTPUT option ;
2531     add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
2532 jmc 1.535 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
2533     allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
2534 heimbach 1.538 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
2535     o add time-dependent SST, SSS control
2536 heimbach 1.539 o cost terms in ecco/ modularized (new cost_generic.F)
2537     o cost_averages routines are modularized (new cost_averagesgeneric.F)
2538     o new infrastructure for seaice model vs. obs misfits in seaice/
2539     * driver from the_main_loop.F is seaice_cost_driver.F
2540     * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
2541     * gradient check in Exp. 6a of natl_box_adjoint/
2542     o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
2543     (see README file)
2544 jmc 1.535
2545 jmc 1.1203 checkpoint57q_post (2005/08/19)
2546 jmc 1.533 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
2547 edhill 1.531 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
2548     - bug was reported by Jean-Michel and Ian Fenty
2549 jmc 1.532 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
2550     update exp. cpl_aim+ocn output.
2551 heimbach 1.530 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
2552     Needed for high-res. runs with large global files
2553     to be able to limit tapelev size
2554     o Changed some tests for adjoint:
2555     * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
2556     * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
2557     * global_ocean.90x40x15/ back to default 3-level checkpointing
2558 heimbach 1.534 o Modifications to enable scripted COMMON to MODULE conversion
2559     * verification/OpenAD/code/ has necessary scripts and description;
2560     * converts, compiles and runs successfully;
2561 heimbach 1.530
2562 jmc 1.1203 checkpoint57p_post (2005/08/01)
2563 jmc 1.529 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
2564     o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
2565     (already the case for some pkgs, including recent MNC_init, e.g. thsice)
2566     o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
2567 jmc 1.527 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
2568     (was already the case for dissipation with mom_vecinv,
2569     and also the case for grad.PhiHyd when staggered-timeStep)
2570     This will allow to put dissipation out-off the AB time-stepping.
2571     Unfortunately, affects truncation error. Update output of exp. that "fails"
2572     (cg2d matching number) and leave the others for later: front_relax(10),
2573     global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
2574     matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
2575    
2576 jmc 1.1203 checkpoint57o_post (2005/07/30)
2577 edhill 1.525 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
2578     (2) its ready to be documented during the 20050801 DocFest
2579 edhill 1.524 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
2580     for ideal_2D_oce and lab_sea on linux_ia32_g77
2581 heimbach 1.526 o set to #undef CTRL_SET_OLD_MAXCVARS_30
2582     in global1x1_tot/code_seaice_adj to access indices 32, 33
2583     (worth another tag)
2584 edhill 1.524
2585 jmc 1.1203 checkpoint57n_post (2005/07/29)
2586 heimbach 1.521 o adding precip control xx_precip 32
2587     o adding swflux control xx_swflux 33
2588 heimbach 1.522 o Replacing 10 forcing penalty cost routines by 1 generic.
2589     o Implementing partitioning in time-mean and variable adjustment
2590     for atmos. state.
2591     o Time-mean constant error is now read in data.ecco (instead of hard-coded)
2592 heimbach 1.519 o in natl_box_adjoint:
2593 heimbach 1.522 * updated exp 1 to 10
2594     (but does not have time-mean vs. variable split results yet)
2595 heimbach 1.523 o updated global1x1/*_seaice_adj/
2596     to incorporate latest changes
2597 heimbach 1.520 o enable useSingleCpuIO for mdsio vector routines
2598     (applies in particular to tapelev I/O)
2599     o removed inefficient K-loop in all active_file*control*.F
2600 heimbach 1.518
2601 jmc 1.1203 checkpoint57m_post (2005/07/28)
2602 jmc 1.516 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
2603     and advect_cs (use EXCH-2 and standard cs-32 grid files).
2604 jmc 1.515 o pkg/exch2: filling of face-corner halo regions is optional
2605     (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
2606    
2607 jmc 1.1203 checkpoint57l_post (2005/07/14)
2608 jmc 1.514 tag before updating tutorials (pre-release-2)
2609 jmc 1.513 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
2610     for output and interpolation of input fields onto model grid)
2611     o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
2612     Affects results of exp. rotating_tank ; update output.txt.
2613 jmc 1.511 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
2614 jmc 1.512 and taking the square quantity and/or using a fraction-weight field.
2615 jmc 1.511 o fix aim_diagnostics_init.F mate numbers.
2616     o add mnc output capability to diagnostics/diagstat and update
2617 edhill 1.510 our cvsignore files for the ACSII output generated
2618    
2619 jmc 1.1203 checkpoint57k_post (2005/07/02)
2620 heimbach 1.509 o lab_sea now uses diagnostics package and provides a suite of
2621     new EXF diagnostics output.
2622    
2623 jmc 1.1203 checkpoint57j_post (2005/06/30)
2624 heimbach 1.508 o exf
2625     * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
2626     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
2627     terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
2628     * extended diagnostics output
2629     - now includes all EXF variables
2630     - hs, hl moved to common block
2631     - separate S/R for diagnostics, called after ctrl vector is added
2632     - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
2633     - EXFqnet contains true Qnet (i.e. includes qsw)
2634     * updated verif. lab_sea, global_with_exf
2635     * Rearranging hflux (exf_mapfields -> exf_getforcing)
2636     to ensure that diagnostics sees a true EXFqnet
2637 jmc 1.507 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
2638 jmc 1.506 o diagnostics pkg: change pointers so that 1 diagnostic can be used
2639     several times with different frequencies.
2640 edhill 1.505 o mnc-ify the thsice package as requested by Daniel Enderton
2641     - the monitor--MNC output needs work
2642     - many attributes need to be added (most are currently blank)
2643     o mnc-ify theaim_v23 package as requested by Daniel Enderton
2644     - many attributes need to be added (most are currently blank)
2645 jmc 1.503 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
2646 jmc 1.502 o add Sadourny like discretization to the 4th.O vorticity advection scheme
2647 jmc 1.500 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
2648 jmc 1.501 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
2649     fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
2650 jmc 1.499 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
2651     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
2652    
2653 jmc 1.1203 checkpoint57i_post (2005/06/19)
2654 molod 1.497 o Diagnostics package was changed: diagnostic allocation is now deactivated
2655     by setting an empty file name in the namelist (used to be by setting 0 frequency)
2656 jmc 1.496 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
2657     add 1rst Order upwind vertical Shear.
2658 edhill 1.495 o add a quick fix for A/B checkpointing in OFFLINE mode
2659 edhill 1.494 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
2660     end-run around the C/Fortran linking horror in eesup/src/timers.F
2661 adcroft 1.493 o added pkg/runclock: allows user to terminate run based on wall clock
2662     o added non-hydrostatic scaling parameter: nh_am2
2663 mlosch 1.492 o pkg/my82: futile attempt to make results compiler-independent by adding
2664     some "_d 0", etc. no effect.
2665 edhill 1.491 o for mnc output, fill the 'T' coordinate var with myTime and create a
2666     separate 'iter' variable for iteration count
2667 jmc 1.489 o pkg/diagnostics:
2668 jmc 1.490 add new capability: output of Global/Regional & per-level statistics ;
2669     tested against monitor output (including land & thSIce) on various exp.
2670     o make seaice-pkg I/O type flags (MNC/MDS) more standard.
2671 jmc 1.489
2672 jmc 1.1203 checkpoint57h_done (2005/05/19)
2673 jmc 1.488 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
2674     data.diagnostics, data.gchem, data.ptracers) is done.
2675    
2676 jmc 1.487 o pkg/diagnostics: prepare for Global/Regional statistics.
2677     add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
2678 jmc 1.486 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
2679     and rename it: DIFFERENT_MULTIPLE
2680    
2681 jmc 1.1203 checkpoint57h_post (2005/05/14)
2682 jmc 1.485 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
2683 jmc 1.484 o pkg/diagnostics: change output frequency, now in seconds (instead
2684     of Nb of iterations). This requires to change data.diagnostics.
2685 jmc 1.1203 checkpoint57h_pre (2005/05/12)
2686 jmc 1.483
2687 edhill 1.482 o in mnc, let the user create the output dir if both mnc_outdir_date
2688     and mnc_outdir_num are false
2689 edhill 1.481 o add fflags() to pkg/diagnostics which allows one to specify, on a
2690     per-file basis, the file precision [default behavior is unchanged]
2691 dimitri 1.480 o added diagnostics to pkg/kpp, including computation of mixed layer
2692     depth based on a temperature/density criterion
2693     o updated verification/natl_box to test the new pkg/kpp diagnostics
2694 jmc 1.479 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
2695 jmc 1.478 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
2696 edhill 1.477 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
2697     not mnc -- this mistake was found by JMC and is now corrected
2698    
2699 jmc 1.1203 checkpoint57g_post (2005/04/15)
2700 jmc 1.476 o add Adams-Bashforth 3rd Order time stepping:
2701     - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
2702     - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
2703 jmc 1.1203 checkpoint57g_pre (2005/04/15)
2704 jmc 1.475
2705 heimbach 1.472 o make lambda[Theta,Salt]ClimRelax spatially varying
2706     (default remains spatially uniform constant based on tau)
2707 heimbach 1.473 o added new control variables
2708     * init. uVel, vVel, etanN
2709     * lambda[Theta,Salt]ClimRelax
2710     o separate masks used for ctrl_pack/unpack 'from write_grid' output
2711     (suggested by G. Forget)
2712 heimbach 1.472
2713 jmc 1.1203 checkpoint57f_post (2005/04/06)
2714 jmc 1.471 o add parameter "baseTime" = model base time = time at iteration zero
2715     new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
2716     account for baseTime shift
2717     o move Coriolis arrays from PARAMS.h to GRID.h
2718 jmc 1.1203 checkpoint57f_pre (2005/04/06)
2719 jmc 1.470
2720 edhill 1.468 o mnc-ifying the seaice package
2721 adcroft 1.467 o introduced an alternative length scale calculation for use in the limiting
2722     maximum viscosity (off by default, see mom_vi_hdissip.F for details)
2723 heimbach 1.466 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
2724 baylor 1.465 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
2725     as well as grad(vort3). Made it compatible with both approximate form
2726     for the cubed sphere and full form of these gradients. Added flag
2727     useFullLeith to select between approximate and full form.
2728 jmc 1.464 o add "d0" in getcon.F to reduce differences between compilers/platforms
2729     update output.txt of exp. fizhi-gridalt-hs
2730 jmc 1.463 o change port_rand funtion to allow to set the seed.
2731 edhill 1.462 o fix obscure MNC bug involving conversion between reals and integers
2732     - it caused no problems with certain (eg. gcc, ifc) compilers but the
2733     new version is now more standards-compliant
2734 heimbach 1.469 o adjoint-related modifications
2735     * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
2736     * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
2737     * mom_vi_hdissip: to be able to use Leith scheme in adjoint
2738 edhill 1.462
2739 jmc 1.1203 checkpoint57e_post (2005/02/28)
2740 heimbach 1.461 o Adding eddy stress controls a la Ferreira et al.
2741 jmc 1.474 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
2742 heimbach 1.460
2743 jmc 1.459 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
2744     update output.txt of exp. fizhi-gridalt-hs
2745 edhill 1.458 o add more "Z" dimensions and associated coordinate vars to MNC
2746 dimitri 1.457 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
2747 dimitri 1.456 o parameter calendarDumps: when set, approximate months (30-31 days) and years
2748     (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
2749     KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
2750     months and years. Requires pkg/cal.
2751 edhill 1.455 o diagnostics: add pickup functionality
2752     - off by default for backwards compatibility
2753     - current version only uses MDSIO -- MNC will be added
2754 jmc 1.454 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
2755 jmc 1.452 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
2756    
2757 jmc 1.1203 checkpoint57d_post (2005/02/11)
2758 jmc 1.451 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
2759 edhill 1.450 o modify verification/ideal_2D_oce so that it tests the creation of mnc
2760     output from the diagnostics package
2761 jmc 1.449 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
2762 edhill 1.448 o make genmake2 more portable by using ".$FS" instead of ".f" for more
2763     of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
2764 edhill 1.447 o add coordinate variables to the MNC output from the diagnostics package
2765 jmc 1.446 o change MNC-flags default value: true when useMNC=TRUE
2766 edhill 1.444 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
2767     the ability (off by default) to read the grid information using MNC
2768 jmc 1.445 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
2769 jmc 1.443 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
2770 jmc 1.442 o do snap-shot diagnostics at the middle of the time-interval (instead of
2771     at the end).
2772 jmc 1.441 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
2773     new test for AIM with thSIce + slab-ocean
2774 jmc 1.440 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
2775 jmc 1.439 o move state variable diagnostics to the beginning of the time step ;
2776     (note: still needs some work specially for snap-shot diagnostics)
2777     duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
2778    
2779 jmc 1.1203 checkpoint57c_post (2005/01/27)
2780 jmc 1.438 o Change testing option (-ieee) to get closer agreement between g77 & ifort
2781     o generate new output.txt files on faulks with g77 & the new -ieee option
2782 jmc 1.1203 checkpoint57c_pre (2005/01/27)
2783 jmc 1.437
2784     o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
2785 jmc 1.436 update output.txt of exp. global_ocean.90x40x15
2786 jmc 1.435 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
2787     results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
2788 jmc 1.432 o add saltFlux(+File) forcing capability with periodicExternalForcing
2789 jmc 1.431 o allow to use pkg diagnostics for GM-Redi & ThSIce output
2790     o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
2791 edhill 1.430 o improvements for the MNC output from DIAGNOSTICS:
2792     - correct handling of the unlimitied dimension
2793     - all dims now have associated coordinate variables
2794     - variables located at U, V, and Corner ("Z") points are now written
2795     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
2796     *all* data points are output
2797 dimitri 1.429 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
2798 dimitri 1.428 o added pkg/seaice/seaice_monitor.F
2799 dimitri 1.427 o mdsio_readfield.F can now read files visible only to master MPI process.
2800 dimitri 1.426 o pkg/seaice: some test code for ice-modified ocean stress
2801 dimitri 1.425 o exf_getffields interpolation defaults to bilinear for all scalar forcing
2802     fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
2803     spurious negative numbers for precipitation and humidity. Will cause
2804     some small numerical differences for integrations using pkg/exf/exf_interp.F.
2805 heimbach 1.434 o pkg/ctrl/
2806     * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
2807     May be enabled via doPackDiag
2808     * introduce z-scaling of
2809     + gradient (doZscalePack) and
2810     + control (doZscaleUnpack)
2811     o pkg/mdsio/
2812     * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
2813     * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
2814 dimitri 1.425
2815 jmc 1.1203 checkpoint57b_post (2004/12/20)
2816 jmc 1.424 o simplify options in diagnostics_fill arguments (remove weird combinations)
2817 edhill 1.423 o fix MNC coordinate variables so that they now contain per-face index
2818     values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
2819     general, EXCH2 grids are only aligned to a "local" coordinate system
2820 jmc 1.422 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
2821     o Implement instantaneous output within pkg diagnostics:
2822     setting a negative frequency in data.diagnostics produces
2823     "snap-shot" output (as opposed to time-average if freq > 0)
2824 jmc 1.421 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
2825     NOTE: change ptracer diagnostics name: use 2 characters to work with
2826     more than 9 tracers. Add also diagnostics of advect & diffus flux.
2827 edhill 1.420 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
2828     becomes the coordinate variable for the 'T' dimension
2829 edhill 1.419 o add CF-style coordinate variables to MNC
2830     - just a first cut: numbers are meaningless on the cubesphere and
2831     missing along the T axis but otherwise it works!
2832 dimitri 1.418 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
2833 jmc 1.417 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
2834 jmc 1.416 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
2835     this is based directly on what the model compute, so that the content of
2836     each diagnostics might be affected by switching options (e.g., implicitDiffusion)
2837     o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
2838 mlosch 1.415 o clean up build options files for SunOS, in particular
2839     - remove -traditional from xmakedepend
2840     - change -xarch=v9 to -xarch=native for f77
2841     - restore use of make (not gmake)
2842     - add CC=gcc if using g77
2843 edhill 1.413 o changes per discussion of AM, JMC, & EH3 today:
2844     - move redundant "grid" variables out of "state" -- in preparation of
2845     creating proper CF-style coordinate variables and in recognition
2846     that any/all grid variables can be easily copied (eg. w/NCO) from
2847     the grid files into any of the other NetCDF files
2848     - *always* output grid variables with MDSIO (this will eventually be
2849     changed)
2850     - output MNC grid file if useMNC is true
2851 edhill 1.412 o every instance of _END_MASTER() has been found and replaced with
2852     _END_MASTER( myThid ) in order to satisfy certain picky Sun
2853     preprocessors
2854 jmc 1.411 o re-arrange diagnostics pkg initialisation:
2855     - allow each package to extend the available diagnostics list
2856     - add some checking and fix small problems (multi-threaded, ...)
2857     - new S/R diagnostics_fill (replace fill_diagnostics):
2858     look through the short list of active diag. (instead of the long list)
2859     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
2860 edhill 1.381
2861 jmc 1.1203 checkpoint57a_post (2004/12/10)
2862 heimbach 1.410 o this set of changes restores TAMC compatibility
2863     tested for global_ocean.90x40x15 adjoint on trough
2864     (what a pain)
2865    
2866 jmc 1.1203 checkpoint57a_pre (2004/12/10)
2867 heimbach 1.409 o some modifs in tools/build_options for sunos
2868     o call ctrl_pack for ctrl at end for optimcycle=0
2869    
2870 jmc 1.1203 checkpoint57 (2004/12/09)
2871 mlosch 1.406 o add horizontal bi-harmonic viscosity for vertical velocity
2872     - new parameter viscA4W (defaults to viscA4)
2873     - affects only non-hydrostatic code
2874     - to be done: no-slip lateral boundary conditions
2875 dimitri 1.405 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
2876 jmc 1.404 o implement Implicit Vertical advection for pTracers
2877 jmc 1.401 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
2878 jmc 1.402 (implemented also for implicit vertical diffusion & advection)
2879 mlosch 1.400 o OBCS: extend application of tracer open boundary conditions
2880     to a strip beyond the boundary of width Olx/Oly
2881 heimbach 1.403 o add call monitor to TAF set of required calls (flow directives)
2882     and include in natl_box_adjoint
2883     o untangle a few ifdefs related to cost, ctrl, autodiff
2884     untangel a few ALLOW_ECCO_OPTIMIZATION
2885 heimbach 1.407 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
2886     (theta2, salt2 in ecco_cost_weights)
2887 mlosch 1.400
2888 jmc 1.1203 checkpoint56c_post (2004/12/03)
2889 mlosch 1.399 o OBCS as control variables
2890     - update ctrl_ad_diff.list, obcs_ad_diff.list
2891     - remove balance of obcs controls from default
2892     - fix index bug nobcs in ctrl_init
2893     - fix dummy fields filen in ctrl_pack
2894     - add dummy weights for obcs
2895     o lsopt: comment out fort.94 output
2896     o optim:
2897     - remove unnecessary header files
2898     - adjusted namelists
2899     - add xerbla.F to Makefile
2900     o exf:
2901     - multiple modifications of exf_check_range
2902     - unit change in exf_init_runoff from [m/year] to [m/s]
2903     o mdsio:
2904     - i/o-vector change debugLevel from debLevA to debLevB
2905    
2906 jmc 1.1203 checkpoint56b_post (2004/12/01)
2907 mlosch 1.397 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
2908     is called from DO_THE_MODEL_IO
2909     - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
2910     - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
2911     - clean up PTRACERS_WRITE_TIMEAVE a little
2912 mlosch 1.396 o add another verification experiment that tests both the cfc-pkg and
2913     the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
2914     reactive tendencies treated inline with regular timestepping
2915 mlosch 1.395 o testreport previously did a lousy job of comparing small numbers, so
2916     we (Ed and Martin) changed the way the cut-off of 1.e-12 is
2917     implemented in the little c-progam tmp_cmpnum.c which is embedded in
2918     testreport.
2919     o ptracers_monitor: bug fix for MPI
2920    
2921 jmc 1.1203 checkpoint56a_post (2004/11/28)
2922 mlosch 1.394 o GCHEM: finish reorganizating the package
2923     - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
2924     (introduces another 3D-array for each passive tracer, but only if
2925     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
2926     gchemTendency is not needed because the timestep is done separately)
2927     - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
2928     - GCHEM is now---more or less cleanly---separate from PTRACERS
2929     - to bo done: handling of surfaceForcingPtr that is needed for KPP not
2930     so clear to me how that should be done in a general way.
2931     o CFC: improve formatting of output in CFC_ATMOS
2932     o PTRACERS:
2933     - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
2934     that ALL experiments with ptracers enable can be checked. This makes
2935     GCHEM_MONITOR obsolete.
2936     - include a runtime parameter PTRACERS_monitorFreq that defaults to
2937     monitorFreq
2938     - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
2939 edhill 1.393 o add PTRACERS (PTR0[1-5]) to testreport output
2940 heimbach 1.391 o exf_check_range:
2941     * default changed to .TRUE.
2942     * will check values for niter0 if debLevA, every timestep if debLevB
2943     * STOP in exf_check_range if 'out of range'
2944     * range chosen generous to allow for potential extema
2945     TBD: a version with stricter range
2946     permitted range would be runtime parameters
2947 jmc 1.390 o GMredi:
2948     - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
2949     - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
2950     - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
2951 mlosch 1.388 o GCHEM:
2952     - move call to GCHEM_FORCING_SEP, so that it is now called before
2953     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
2954     - introduced a useGCHEM runtime flag and applied it everywhere.
2955 mlosch 1.392 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
2956     this flag is now only visible within GCHEM-pkg routines.
2957     - moved gchem_forcing_int temporarily into ptracers_forcing, this will
2958     be replaced by a 3D array that is computed before thermodynamics; for
2959     this, the tracer ID iTracer had to be included into the parameter list
2960     of ptracers_forcing
2961 mlosch 1.394 - set up forward_step to call gchem_forcing, that will replace
2962 mlosch 1.392 gchem_forcing_int in ptracers_forcing
2963     - cleaning up
2964 jmc 1.389 o small cleaning of exch2: remove files that are also in eesupp/src
2965 mlosch 1.387
2966 jmc 1.1203 checkpoint56 (2004/11/17)
2967 jmc 1.385 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
2968 edhill 1.384 o mnc: cleanup "full" files--fixes out-of-memory problem
2969 heimbach 1.386 o ECCO-GODAE
2970     * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
2971     * fully merged and updated from SIO code
2972     windstress sign change affects
2973     - exf_inscal_[u/v]stress
2974     - sign of xx_tau[u/v] adjustments
2975     - signs in cost_scat
2976     * ctrl_get_gen: avoid update of tau[u/v] for first few days
2977     * natl_box_adjoint updated and compressed
2978     * 2-level checkpoint switch added
2979     (tested in EXP. 1 of natl_box_adjoint)
2980     * new switch doInitXX to avoid init. of xx_... in optimcycle=0
2981     o SVD
2982     * first complete, non-hacked version for SVD calculations
2983     * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
2984     performed via direct access files admtlm_vector.it????
2985     (via ctrl_[un]pack)
2986     * optimcycle is used for ARPACK iteration counter
2987     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
2988     * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
2989     and add linear transforms where necessary
2990     * controls are initial/final SST, SSS (can be extended; need to check
2991     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
2992     o mdsio: filename info to both stderr, stdout
2993     o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
2994     from sign change
2995 edhill 1.384
2996 jmc 1.1203 checkpoint55j_post (2004/11/10)
2997 jmc 1.382 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
2998     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
2999 edhill 1.381 o add consistent build directories and .cvsignore files to verification
3000 dimitri 1.380 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
3001 edhill 1.379 o make all subroutines 30 or less characters in length for certain older
3002     compilers to work (a thorough search only turns up two routines in
3003     pkg/ptracers)
3004 jmc 1.378 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
3005     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3006    
3007 jmc 1.1203 checkpoint55i_post (2004/10/28)
3008 jmc 1.376 o change arrays for total vertical diffusivity (2.D if explicit,
3009     3.D if implicit) ; each ptracer uses its own background value.
3010 edhill 1.375 o added mnc/NetCDF output capability to ocn_compon_interf
3011     - added bits to verification/cpl_aim+ocn so that it can run on
3012     ITRDA and other clusters without the mpirun "-wd" option
3013 afe 1.374 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
3014     configuration
3015 edhill 1.373 o give MNC the ability to create additional files rather than
3016     exceeding a specified file size limit "MNC_MAX_FILESIZE"
3017     - the default is just less than 2GB which is a practical limit
3018     on many systems
3019 jmc 1.372 o Compute the non-local term using either KPP vertical diffusivity (=default)
3020     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
3021 jmc 1.349
3022 jmc 1.1203 checkpoint55h_post (2004/10/20)
3023 jmc 1.371 o add verification test "vermix"
3024 edhill 1.370 o remove all the *_ioinc flags and replace with the single global
3025     outputTypesInclusive flag
3026 jmc 1.369 o allow to set a vertical profile of vertical diffusivity for T & S
3027 jmc 1.371 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
3028     o useMNC moved from data.mnc to data.pkg
3029 jmc 1.369
3030 jmc 1.1203 checkpoint55g_post (2004/10/14)
3031 heimbach 1.368 o Renaming carbon AD experiments to comply with testreport conventions
3032     o Updating adjoint of Held-Suarez hs94.1x64x5
3033     o Fixing directives for non-ECCO forward_step, after ECCO directives
3034     have been fixed to avoid recomp. of do_oceanic_phys
3035     Works well for global_ocean.90x40x15,
3036     but recomp. issue remains for carbon
3037     o Updating adjoint output for natl_box_adjoint after
3038     pkg/ecco has been modified (see taga c55d_post)
3039    
3040 jmc 1.1203 checkpoint55f_post (2004/10/13)
3041 edhill 1.367 o rename to timeave_init_fixed
3042    
3043 jmc 1.1203 checkpoint55e_post (2004/10/13)
3044 heimbach 1.366 o some delicate re-shuffle of store directives to avoid one
3045     extra call of do_oceanic_physics
3046     affects ecco_the_main_loop.F, do_oceanic_physics.F
3047     checkpoint_lev1_directives.h
3048     o NB: this may break global_ocean adjoint temporarily,
3049     but it is clear how to fix it. Will do later, need this now.
3050    
3051 jmc 1.1203 checkpoint55d_post (2004/10/11)
3052 heimbach 1.365 o ECCO specific cost function terms (up-to-date with 1x1 runs)
3053     o ecco_cost_weights is modified to 1x1 runs
3054     o modifs to allow observations to be read in as
3055     single file or yearly files
3056     o enable to read exf forcing fields as either
3057     single file or yearly files (flag useExfYearlyFields)
3058 jmc 1.1203 checkpoint55d_pre (2004/10/08)
3059 heimbach 1.365
3060     o switch between 2-level and 3-level checkpointing
3061 edhill 1.364 o add ability of MNC to write local and "partial" (eg. 2D slices where
3062     the full 3D field is never actually stored) arrays to NetCDF files
3063     with the correct (that is, the complete multi-dimensional) set of
3064     array indicies
3065     - used in mom_vecinv() to write the diagFreq output
3066     - tested (demonstrated) in verification/aim.5l_cs
3067 edhill 1.363 o further mnc-ification
3068     - add verification/lab_sea to the list with mnc setups
3069     - fix undefined mnc v-names in cd_code
3070     - add kpp to mnc output (both snapshot and timeave)
3071 mlosch 1.362 o non-hydrostatic code
3072     - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
3073     in calc_gw.F
3074     - defaults to viscAh
3075     - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
3076     friction or Leith) in non-hydrostatic mode, as long as there is
3077     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
3078 heimbach 1.360 o pkg/cost
3079     extend simple cost functions to treat time mean quantities
3080     (T,U,V) via cost_accumulate_state from cost_tile
3081 jmc 1.358 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
3082     be 2 times larger than the minimum size the advection scheme requires.
3083     now get a perfect conservation of salt in advect_cs test-exp (updated)
3084 mlosch 1.356 o GGL90 (Gaspar's TKE mixed layer)
3085     - add horizontal diffusion of TKE, requires exchanges in
3086     do_fields_blocking_exchanges, horizontal diffusivity is zero by
3087     default. In OPA there is no horizontal diffusion of TKE but the
3088     mixing coefficients are computed from a horizontal average of TKE of
3089     6 points or so. I think that diffusion has a little more physical
3090     justification.
3091     - clean up ggl90_calc in the hope of reducing memory usage (this hope
3092     was in vain)
3093     - mask tke-variable in ggl90_init
3094 jmc 1.355 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
3095     o fix biharmonic diffusion on CS-grid.
3096 mlosch 1.354 o more obcs stuff
3097     - added obcs_external_fields_load as an alternative to the EXF-pkg option
3098     for reading boundary values. This routine is called from
3099     obcs_prescribe_read
3100     - updated obcs_check
3101 mlosch 1.357 - changed sponge layer relaxation parameter units for days to seconds
3102     - turned off sponge layer by default
3103 heimbach 1.359 - changed argument list of OBCS_CALC to myTime+deltaTclock
3104 mlosch 1.361 - fixed about 35 bugs in obcs_external_fields_load
3105 mlosch 1.354
3106 jmc 1.1203 checkpoint55c_post (2004/09/23)
3107 heimbach 1.352 o obcs stuff
3108     - new runtime flags useOBCSprescribe, useOBCSbalance
3109     - re-arranged obcs_calc
3110     - moved exf_getobcs to obcs_prescibe_read
3111     obcs_prescibe_read is called after ORLANSKI stuff
3112     and independent of it (executable can contain all).
3113     - updated obcs_check
3114 heimbach 1.353 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
3115     These may be necessary only if tangential velocities are
3116     prescribed at OB, not sure, needs testing.
3117 edhill 1.351 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
3118     which simplifies the calls and passes the ifc check-bounds test
3119    
3120 jmc 1.1203 checkpoint55b_post (2004/09/22)
3121 jmc 1.350 o add a 2D scalar, Z location, exchange_2 routine.
3122 jmc 1.349 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
3123     to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
3124     affects advect_cs results (for the wrong reason): update output.txt
3125 jmc 1.348 o use a more standard discretization for biharmonic viscosity ;
3126     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
3127     affects results of dome set-up: update output.txt
3128     o fix gad_advection.F (CubedSphere part), back to version 1.23
3129     o fix bug in mom_vi_del2uv.F (CubedSphere part).
3130 mlosch 1.341
3131 jmc 1.1203 checkpoint55a_post (2004/09/20)
3132 heimbach 1.347 o merged code to
3133     * prescribe/read time-dependent open boundaries
3134     (works in conjunction with exf, cal)
3135     * sponge layer code for open boundaries
3136     * each boundary N/S/E/W now has its own CPP option
3137     (healthy for the adjoint)
3138    
3139 jmc 1.1203 checkpoint55 (2004/09/17)
3140 heimbach 1.346 o up-to-date adjoint of previous breaks
3141     - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
3142     - global_ocean_ebm: adjoint still needs fix (TLM ok)
3143     - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
3144     - carbon: * remove tr1-related adjoint verification
3145     * add ptracer as control variable
3146     o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
3147     (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
3148    
3149 jmc 1.1203 checkpoint54f_post (2004/09/16)
3150 heimbach 1.345 o in verification/carbin/ remove experiment related to
3151     ALLOW_PASSIVE_TRACER (array tr1 etc)
3152     code_ad/ input_ad/ results_ad
3153    
3154 mlosch 1.344 o add two new packages
3155     - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
3156     + subject to optimization (memory)
3157     - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
3158     + subject to reordering (many GOTOs in the original code)
3159     + so far opps is called for every (i,j) point, and then operates in
3160     the vertical; one may want to reorder the scheme in order operate in
3161     horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
3162     fields)
3163 edhill 1.343 o overhaul of IO so that we now have flags for MDSIO and/or MNC
3164     - all verification tests compile and run with linux_ia32_g77
3165     - defaults are compatible with current input files--nothing
3166     should change if you were not previously using MNC
3167     - MNC output has been added in numerous places (eg. timeave)
3168     but there are still a few writes not yet do-able with MNC
3169     (this is in progress)
3170     - flags now allow for either/or/both use of MDSIO and MNC and
3171     documentation will soon follow
3172     - numerous small formatting cleanups for ProTeX
3173 edhill 1.342 o add version info (via BUILD_INFO.h) to MNC and stdout
3174    
3175 jmc 1.1203 checkpoint54e_post (2004/09/02)
3176 mlosch 1.341 o add two new packages
3177     - pp81 (Packanowski and Philander, 1981), Richardson number and
3178     stratification dependent mixing
3179     - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
3180     - these scheme operate in a similar manner as KPP (without ghat, of
3181     course), however there is only one diffusivity that is used for both
3182 mlosch 1.1068 temperature and salinity (and passive tracers)
3183 stephd 1.340 o add offline package
3184 edhill 1.339 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
3185     provided by Stephanie Dutkiewicz
3186 edhill 1.338 o genmake2: add ability to search for C compilers and cleanup test output
3187     - fixes recent SX-6 problems and should help with others (eg. HP-UX)
3188    
3189 jmc 1.1203 checkpoint54d_post (2004/07/27)
3190 adcroft 1.336 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
3191 jmc 1.337 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
3192     leading to additional shift by 5 days each year of integration
3193     (i.e. leading to considerable offset over the years)
3194 jmc 1.335 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
3195     o start with no AB and no initial filtering (staggerTimeStep):
3196     change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
3197     o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
3198     (external loading & cpl import/export stay in forward_step.F)
3199     o update coupling interface to work with new staggerTimeStep
3200     o change MDSIO ptracers_pickup.
3201 jmc 1.334 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
3202 edhill 1.333 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
3203 jmc 1.334 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
3204 edhill 1.333
3205 jmc 1.1203 checkpoint54c_post (2004/07/18)
3206 jmc 1.331 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
3207     this affects (truncation error) output.txt of test-exp:
3208     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
3209     o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
3210 jmc 1.330 o change Qnet to always be the net heat flux, (+upward).
3211     affects (truncation error) output of natl_box exp.: updated
3212 jmc 1.329 o define the max number of passive tracers in PTRACERS_SIZE.h
3213     o start to test mnc routinely in exp0
3214     o add sea-ice loading (sIceLoad) as a new forcing field.
3215    
3216 jmc 1.1203 checkpoint54b_post (2004/07/08)
3217 edhill 1.327 o add testreport "-j JOBS" option for parallel builds (tested and pretty
3218     impressive on Altix and Opteron systems)
3219 edhill 1.326 o diagnostics can now write NetCDF files through the mnc package
3220 jmc 1.325 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
3221 jmc 1.324 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
3222 jmc 1.323 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
3223     affects (truncation error) output of lab_sea & natl_box exp.: updated
3224     o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
3225    
3226 jmc 1.1203 checkpoint54a_post (2004/07/06)
3227 jmc 1.322 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
3228     o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
3229     o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
3230     o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
3231     + internal_wave (shift in writing cg2d_ini_res)
3232 jmc 1.1203 checkpoint54a_pre (2004/07/05)
3233 jmc 1.321
3234 dimitri 1.320 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
3235     - modified verification/lab_sea and natl_box_adjoint accordingly
3236    
3237 jmc 1.1203 checkpoint54 (2004/07/02)
3238     checkpoint53g_post (2004/07/02)
3239 jmc 1.317 o prepare splitting of thermodynamics: store convect.counter in common block
3240 jmc 1.316 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
3241     output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
3242 dimitri 1.315 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
3243 jmc 1.314 o new parameter "nShapS": allow to treat differently S from T (nShapT)
3244     o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
3245 heimbach 1.318 o restore adjointability
3246 jmc 1.314
3247 jmc 1.1203 checkpoint53f_post (2004/06/25)
3248 jmc 1.313 o modifications that affect AIM experiment results (update output.txt):
3249     - no advection of S at top interface Nr (pkg/generic_advdiff)
3250     - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
3251 jmc 1.312 o AIM pkg:
3252     - include stability function into surf.Flux derivative relative to Tsurf
3253     - calculate clear-sky radiation & surface temp. change (for diagnostics)
3254 jmc 1.313
3255 afe 1.311 checkpoint53e_post
3256     o merged cylindrical coord configuration
3257     o added rotating_tank experiment
3258 afe 1.310 checkpoint53e_pre
3259    
3260 jmc 1.1203 checkpoint53d_post (2004/06/14)
3261 jmc 1.308 o faulks upgraded: re-generate output.txt that have changed:
3262     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
3263 adcroft 1.307 o Added Bryan and Lewis, 1979, vertical diffusivity profile
3264 jmc 1.306 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
3265 adcroft 1.305 o added Sadourny discretization of Coriolis
3266     - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
3267     - re-enabled use of omega3 (useAbsVorticity)
3268 adcroft 1.304 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
3269 jmc 1.309 vector-invariant equations
3270 adcroft 1.304 - note: does *NOT* yet use same variable visc. for no-slip BC's.
3271 mlosch 1.303 o recoded the lateral boundary conditions for non-hydrostatic w, this time
3272     hopefully without new bugs
3273     - still to do: biharmonic friction for non-hydrostatic w
3274 adcroft 1.302 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
3275     o regenerated output for global_ocean_ebm (using -ieee)
3276 adcroft 1.301 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
3277     of mom_common/
3278     - simple re-arrangement of instructions within computing loop
3279 jmc 1.1203 checkpoint53d_pre (2004/05/21)
3280 mlosch 1.297
3281 jmc 1.1203 checkpoint53c_post (2004/05/21)
3282 jmc 1.299 o new version of coupler for AIM+thSIce and Ocean models
3283     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
3284     - land: change Evaporation of snow
3285     - aim with thSIce: fix bug in snow-precip.
3286 mlosch 1.297 o changes to calc_gw.F
3287     - bug fix for w^2 term near the bottom boundary
3288     - (hopefully) improve the lateral slip boundary condtions for use with
3289     partial/looped cells
3290     - because the bug fix changes two verification experiments anyway (exp5
3291     and plume on slope), change the lateral boundary condition from half slip
3292     to the value of no_slip_sides
3293 heimbach 1.298 o ebm package wasnt quite up to the parallel task. Fixed that.
3294 heimbach 1.300 o Adjoint of EBM package + verification
3295     * TLM OK
3296     * ADM not sufficient accuracy yet (needs further testing)
3297 heimbach 1.295
3298 jmc 1.1203 checkpoint53b_post (2004/05/14)
3299 heimbach 1.296 o Commiting new energy balance model to repository
3300     * package is pkg/ebm
3301     * verif. is verification/global_ocean_ebm
3302     * references are in ebm_driver.F
3303     C * X. Wang, P. Stone and J. Marotzke, 1999:
3304     C Global thermohaline circulation. Part I:
3305     C Sensitivity to atmospheric moisture transport.
3306     C J. Climate 12(1), 71-82
3307     C * X. Wang, P. Stone and J. Marotzke, 1999:
3308     C Global thermohaline circulation. Part II:
3309     C Sensitivity with interactive transport.
3310     C J. Climate 12(1), 83-91
3311     C * M. Nakamura, P. Stone and J. Marotzke, 1994:
3312     C Destabilization of the thermohaline circulation
3313     C by atmospheric eddy transports.
3314     C J. Climate 7(12), 1870-1882
3315     o Will need long integration testing.
3316 jmc 1.1203 checkpoint53b_pre (2004/05/14)
3317 dimitri 1.292
3318 adcroft 1.294 o created pkg/mom_common in preparation for variable viscosity code
3319     o renamed and split ini_mnc_io
3320 jmc 1.293 o pkg/land: only liquid water can diffuse or run-off
3321     o AIM using land: soil wetness availability account for snow
3322 dimitri 1.292 o added printMapIncludesZeros to EEPARMS namelist
3323 heimbach 1.290
3324 jmc 1.1203 checkpoint53a_post (2004/05/11)
3325 heimbach 1.290 o restore TAMC compatiility for exf_constants.h
3326     (no usage of _d in .h)
3327     o Additional storing in KPP in an attempt to fix
3328     TAMC problem with adjoint of KPP code.
3329     (no success...)
3330     Identical code works fine with TAF.
3331 dimitri 1.291 o Fixed verification/natl_box_adjoint experiments.
3332     Initial conditions for Experiments 4 and 5 are now
3333     set to "SEAICE_initialHEFF=0", which is more reasonable,
3334     and hence gives results closer to that of Experiment 2.
3335     Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
3336 cnh 1.289
3337 jmc 1.1203 checkpoint53 (2004/05/06)
3338 cnh 1.289 o stable checkpoint with up to date adjoint
3339     TLM tests only run for 1st grdchk at the moment. Its unclear if
3340     this is a code problem or a problem with resetting code for g_
3341     variables that is being autogenerated wrong.
3342     Otherwise:
3343     o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
3344     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
3345     are both still in chaos following their security messes.
3346 jmc 1.279
3347 jmc 1.1203 checkpoint52n_post (2004/05/06)
3348 edhill 1.288 o various build (mostly genmake2) changes including:
3349     - ability to build/run more easily within Cygwin and MacOS X
3350     - more complicated Makefiles with a stronger dependence on Gnu Make
3351 dimitri 1.285 o pkg/seaice modifications
3352 dimitri 1.287 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
3353     of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
3354     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
3355 dimitri 1.285 - changed proxy for geostrophic velocity and updated
3356 dimitri 1.286 verification/lab_sea/results/* accordingly
3357 dimitri 1.285 - removed ADI dynamic solver from pkg/seaice
3358     - replaced all occurrences of 1/CSTICE or 1/CSUICE
3359     they caused a segmentation fault under certain circumstances
3360 mlosch 1.283 - removed unused field WATR
3361 mlosch 1.282 o bug fix in exf-package:
3362     - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
3363     now reflect that.
3364 mlosch 1.281 o small fixes in the cal-package:
3365     - set reference date to first of January for the 'model'-calendar
3366     - failing of cal_CheckDate in cal_FullDate now actually results in a
3367     warning
3368 mlosch 1.280 o small modifications in exf-package to increase flexibility:
3369     - change climtempfreeze from a constant to a runtime parameter that
3370     is specified in data.exf_clim (default = -1.9)
3371     - introduce runtime parameter windstressmax (default = 2.0) that is
3372     specified in data.exf
3373 jmc 1.279 o fix in pkg/thsice:
3374     - update Evap (Tsf changes) to be consistent with Latent heat flux
3375     - maintain snow precipitation unchanged (even if Tsf >=0).
3376     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
3377 edhill 1.272
3378 jmc 1.1203 checkpoint52m_post (2004/04/18)
3379 mlosch 1.277 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
3380     this does not change any of the results, because myIter=0 in swfrac always
3381     lead to jwtype=2 (the default anyway), but the call makes little sense
3382     as a default
3383 jmc 1.276 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
3384 jmc 1.275 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
3385     atmospheric model (AIM) to use it ; add a "slab ocean" component.
3386     o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
3387     o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
3388 dimitri 1.274 o extending useSingleCpuIO option to work with new exch2 I/O format
3389     - old-style, missing-tile I/O is still accessible by defining CPP
3390     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
3391 edhill 1.273 o monitor package can write to NetCDF files and/or STDOUT
3392     o fix re-definition bug in MNC_GRID_INIT_ALL()
3393 edhill 1.272 o doc/api_reference added
3394     - a framework for building an API Reference Manual using all
3395     the "protex" comments embedded in the code
3396     - see pkg/generic_advdiff, pkg/mnc for examples
3397 edhill 1.269 o MNC:
3398     - make myThid the last argument for all subroutines
3399     - new default for the grid files: NO halos
3400 edhill 1.270 - add useMNC and other run-time flags
3401     - separate per-file-group handling of the unlimited dimension
3402     - early initialization of MNC w/ flags read at the eeboot stage
3403     and lookup tables set in initialize_fixed
3404     - write all MNC output to a freshly-created directory
3405 jmc 1.268 o thermodynamics sea-ice (thsice) is now tested with testreport.
3406     o test exp. advect_cs: use the standard cs32 grid ; update output.
3407 heimbach 1.271 o Added functionality to grdchk:
3408     pick global i,j,k position (or nearest wet) where to perform check.
3409 jmc 1.266
3410 jmc 1.1203 checkpoint52l_post (2004/03/11)
3411 jmc 1.267 o new land formulation:
3412     a) use ground enthalpy as prognostic variable to ensure exact
3413     energy conservation.
3414     b) account for water temperature and for latent heat of freezing
3415     in all processes (rain, run-off, ground storage)
3416     c) compute surface and ground temperature implicitly.
3417     o aim_v23 modification for new land model:
3418     a) Treat separately land / ocean / sea-ice surface fluxes
3419     to allow implicit computation of land & sea-ice surface temp.
3420     b) add snow precipitation.
3421 jmc 1.1203 checkpoint52l_pre (2004/03/11)
3422 jmc 1.266
3423 jmc 1.265 o fix problem (when 1 tile is empty) in min/max monitor.
3424     o fix bug in timeAve (u,vZetatave in common block)
3425 dimitri 1.264 o no restoring terms under ice for pkg/seaice
3426 dimitri 1.263 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
3427     o bug fix for pkg/seaice pickups
3428 edhill 1.262 o change MNC call locations and add coordinate attributes
3429 jmc 1.260 o mask vorticity at the corner ; affects global_ocean.cs output
3430     o fix ini_curvilinear_grid ; test CS experiments with mpi
3431 jmc 1.259 o aim.5l_cs: modify sea-ice fraction input file ; update output
3432 heimbach 1.261 o exf: Adding simple range check routine for exf fields after read
3433 adcroft 1.256
3434 jmc 1.1203 checkpoint52k_post (2004/02/23)
3435 adcroft 1.256 o removed top-level directory "diags"
3436     - we migrated these functions to pkg/timeave a long time ago
3437     o fixed bug introduced in pkg/monitor
3438 heimbach 1.257 o accuracy ctrlprec = 32 insuffient for gradient checks using
3439     averaged fields (I/O via cost_averages)
3440     -> use ctrl.h in active_file*.F to control I/O precision.
3441     o paramter list of CALL ADTHE_MAIN_LOOP
3442     o added initial do_the_model_io to ecco
3443     o set all ...Freq to zero after cost_final
3444     taveFreq, dumpFreq, pChkptFreq
3445 heimbach 1.258 o MAIN and ECCO differentiability restored
3446 heimbach 1.255
3447 jmc 1.1203 checkpoint52j_post (2004/02/18)
3448 heimbach 1.255 o fix nchklev in tamc.h for global_ocean...
3449     o Bringing flow and store directives up-to-date
3450     o Really weird thing!
3451     call do_the_model_io from the_main_loop with parameters
3452     starttime, niter0, instead of mytime, myiter, screws up the adjoint:
3453     TAF places a faulty re-call of initialise_varia
3454     after cost_final call which should not be there!
3455 jmc 1.1203 checkpoint52j_pre (2004/02/03)
3456 jmc 1.253
3457 afe 1.254 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
3458     error messages
3459 jmc 1.253 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
3460 afe 1.252 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
3461     debug output
3462 afe 1.251 o modfied mdsio_writefield.F to handle non-global files under exch2
3463 jmc 1.250 o update AIM Cubed-Sphere exp (aim.5l_cs):
3464     use land, p*, and Franco.M forcing fields with fractional land-sea mask.
3465     o update AIM Equatorial Channel exp:
3466     use standard aim_v23 pkg and change the SST fields to be more realistic.
3467 afe 1.248 o globalFile now works with exch2
3468 afe 1.247 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
3469 jmc 1.253 mon_vort3.F to make exch2 friendly with >1 tile per cube face
3470 dimitri 1.249 o limit timeave output for hi-res integrations
3471 adcroft 1.245
3472 jmc 1.1203 checkpoint52i_post (2004/01/21)
3473 adcroft 1.245 o removed CPP_EEOPTIONS.h from verification/*/code
3474     o updated the tiling for global_ocean_pressure
3475 jmc 1.1203 checkpoint52i_pre (2004/01/20)
3476 jmc 1.246
3477     o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
3478     the old pkg/aim).
3479 afe 1.239
3480 jmc 1.1203 checkpoint52h_pre (2004/01/20)
3481 afe 1.243 o shortened offending lines in exch2_send_rx?.template
3482 afe 1.242 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
3483 edhill 1.240 o genmake2: add build & execute test for NetCDF code
3484 afe 1.239 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
3485     old grid files, moved CPP_EEMACROS.h to pkg/exch2
3486 dimitri 1.238 o added useSingleCPUIO flag to monitor.F and mon_out.F
3487 dimitri 1.241 o added temporary hack for sea-ice dynamics on the cube:
3488     metric terms are ignored and it is assumed that
3489     there is no sea-ice on cube faces 1, 2, 4, and 5.
3490 dimitri 1.238
3491 jmc 1.1203 checkpoint52f_post (2004/01/09)
3492 afe 1.236 o added exch2 cube routines to pkg/exch2
3493     o modified hs94.cs-32x32x5 to use it
3494     o added new grid files to hs94.cs-32x32x5
3495 jmc 1.1203 checkpoint52f_pre (2004/01/07)
3496 dimitri 1.228
3497 jmc 1.1203 checkpoint52e_post (2004/01/07)
3498 jmc 1.234 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
3499     for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
3500 jmc 1.235 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
3501     to work with implicit vertical advection and AB ;
3502     o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
3503     o update output (gad_calc_rhs.F changes affect truncation error) of exp:
3504     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
3505 jmc 1.1203 checkpoint52e_pre (2004/01/02)
3506 jmc 1.233
3507     o fix bug in impldiff when Nr=1 or Nr=2.
3508 jmc 1.232 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
3509     o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
3510 jmc 1.229 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
3511     ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
3512 dimitri 1.228 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
3513 dimitri 1.231 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
3514     o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
3515 jmc 1.220
3516 jmc 1.1203 checkpoint52d_post (2003/12/16)
3517 adcroft 1.230 o re-tiled many expts to allow comparison in multi-processor mode
3518     - updated output accordingly
3519     - changed hs94.128x64x5 to use intial T from file rather than use the
3520     random number generator
3521 molod 1.227 o add infrastructure in model routines for fizhi and gridalt packages
3522 jmc 1.220 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
3523 dimitri 1.222 o changes to permit hi-res, cubed-sphere, configuration
3524     - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
3525     - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
3526     - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
3527     of surface winds for the cube
3528     (A verification experiment, based on global_ocean.cs32x15, but with
3529     pkg/seaice turned on and with on-the-fly interpolation from the NCEP
3530     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
3531     complete with example surface forcing files and matlab scripts to look
3532     at the output and compare it with that of global_ocean.cs32x15.)
3533 jmc 1.223 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
3534     but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
3535     to conform to the common rule.
3536 jmc 1.224 o check-in the first version of the coupler + interfaces for multi-components
3537     set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
3538     - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
3539     - atmosphere: use pkg aim_v23 ; no sea-ice for now.
3540     - ocean and atmos. share the same horizontal grid (no interpolation).
3541     - exchanges between component and coupler is done in forward_step
3542 jmc 1.225 o new verification experiment, cpl_aim+ocn:
3543     coupled ocean - AIM atmosphere on cs32 grid.
3544 jmc 1.217
3545 jmc 1.1203 checkpoint52d_pre (2003/12/06)
3546 jmc 1.217 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
3547 jmc 1.218 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
3548 heimbach 1.213
3549 jmc 1.1203 checkpoint52c_post (2003/11/25)
3550 heimbach 1.213 o Fixing OPTIONS files for use of exf:
3551     - ALLOW_ECCO not needed
3552     - ECCO_CPPOPTIONS.h should not be included from
3553     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
3554     as has been the case in the past
3555     - All cal/exf related options are currently set in
3556     single header file. Should remain so until we
3557     agree on a consistent new policy.
3558 heimbach 1.214 o Removed all CPP options for cal package.
3559     cal has no more CPP options.
3560 heimbach 1.215 o modified STOREs in GAD_ADVECTION
3561     o corrected key comp. for passkey
3562 heimbach 1.210
3563 jmc 1.1203 checkpoint52b_post (2003/11/23)
3564 jmc 1.212 o new version: "thsice" of thermodynamic sea-ice pkg:
3565     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
3566     - modify fluxes but do not change theta directly;
3567     - light cleaning of bulk_force pkg (still needed with thsice).
3568     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
3569     + output_thsice.txt to test thsice & bulk_force pkgs.
3570     o put back grid & coriolis monitor output.
3571 jmc 1.1203 checkpoint52b_pre (2003/11/23)
3572 jmc 1.211
3573     o call "do_the_model_io" at the beginning (=> dump initial state)
3574     o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
3575 heimbach 1.210 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
3576     (need info on NUMBER_OF_PTRACERS)
3577     o missing PTRACERS headers in some routines
3578     o default tamc.h in pkg/autodiff supposed to crash
3579     to ensure proper customization
3580 dimitri 1.206
3581 jmc 1.1203 checkpoint52a_post (2003/11/17)
3582 jmc 1.208 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
3583 dimitri 1.207 - moved surfaceTendencyTice from pkg/seaice to main code
3584 jmc 1.208 - subroutine FREEZE_SURFACE now limits only surface temperature
3585     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
3586     => new output.txt for global_ocean.cs32x15 & global_with_exf
3587     - keep the old version of FREEZE for backward compatibility;
3588     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
3589 heimbach 1.209 - corresponding modifs for TAF directives
3590 dimitri 1.207 o added surface flux output variables to TIMEAVE_STATVARS
3591     o time-averaged output for pkg/ptracers
3592 heimbach 1.209 o fix problem with ECCO-related divided adjoint
3593     snapshot file was missing some ad-variables,
3594     but no warning issued by TAF
3595 dimitri 1.206
3596 jmc 1.1203 checkpoint52a_pre (2003/11/12)
3597 dimitri 1.206 o some bug fixes for #undef REAL4_IS_SLOW
3598 heimbach 1.205
3599     checkpoint52 = ecco_c52_e35
3600     o after testing adjoints of checkpoint51u_post
3601 edhill 1.203
3602 jmc 1.1203 checkpoint51u_post (2003/11/06)
3603 heimbach 1.204 o this is the post-merge tag of the ecco-branch
3604     (needs another clean checkout and re-testing)
3605     o various natl_box_adjoint configs and results
3606     but no input fields
3607     o obcs adjoint not yet merged!
3608     o adding ECCO global 1x1 and 2x2 degree configs
3609     o updated/extended some store directives for seaice
3610     o pkg/ecco now containes ecco-specific part of cost function
3611     o top level routines the_main_loop, forward_step
3612     supersede those in model/src/
3613     previous input data.cost now in data.ecco
3614     (new namelist ecco_cost_nml)
3615     o in ctrl/ cleaned some cross-dependencies and updated CPP options
3616    
3617 jmc 1.1203 checkpoint51t_post (2003/11/04)
3618 heimbach 1.204 o this is the pre-merge tag of the ecco-branch
3619    
3620 jmc 1.1203 checkpoint51s_post (2003/11/04)
3621 edhill 1.203 o cleanup: removed various obsolete #define-s
3622 heimbach 1.204 o pkg/grdchk
3623     - renamed 'ph-grd 3' to 'grad-res'
3624     - merged from ecco-branch
3625     (remaining bug fixes for obcs gradient checks)
3626     - additional high-precision output for testreport
3627     (grep for 'precision_grdchk_result')
3628 edhill 1.202
3629 jmc 1.1203 checkpoint51r_post (2003/11/03)
3630 edhill 1.202 o cleaned up or removed CPP_OPTIONS.h files
3631     o updated results for some of the tests to reflect the new
3632     optfiles (-ieee: -O0 instead of -O3)
3633 heimbach 1.201
3634 jmc 1.1203 checkpoint51q_post (2003/10/30)
3635 heimbach 1.201 o cd_code:
3636     - moved cd_scheme.F -> cd_code_scheme.F
3637     - separate read_checkpoint from cd_code_ini_vars.F
3638     - separated cd_code part from write_checkpoint
3639     - updated AD_SOURCE, generated .flow
3640     - added CD_CODE_VARS.h to the_main_loop
3641     - Moving cd_code specific store dir.s to pkg/cd_code
3642     o ctrl package totally restructured
3643     - pack/unpack now optional and decoupled from
3644     xx_/adxx_ I/O
3645     - ctrl_pack/unpack cleaned
3646     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
3647     - confined inclusion of AD_CONFIG.h to where necessary.
3648     o genmake2: changed AD dependencies from SRCFILES to AD_FILES
3649 edhill 1.198
3650 jmc 1.1203 checkpoint51p_post (2003/10/30)
3651 edhill 1.198 o create initial cd_code package
3652 edhill 1.199 - WARNING: the initialization of fields within packages
3653     is broken because INI_FIELDS (where READ_CHECKPOINT is
3654     called) is called *before* PACKAGES_INIT_VARIABLES.
3655     This seems to be backwards since
3656     1) its important to initially zero the entire field including
3657     the "halo" region
3658     2) zeroing needs to be done *before* reading pickup info
3659     and the pickup call might or might not happen in any
3660     particular run
3661     - this needs an overhaul for R2
3662 edhill 1.198 o cleanup verification/*/code/GMREDI_OPTIONS.h
3663     o cleanup testreport
3664 heimbach 1.196
3665 jmc 1.1203 checkpoint51o_post (2003/10/27)
3666 heimbach 1.196 o bringing AD-related verif's up to date with genmake2
3667     - carbon/
3668     - global_ocean.90x40x15/
3669     - hs.94.1x64x5/
3670     - (front_relax/ )
3671     o (more) consistent directory structure for AD-related verif.'s
3672     o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
3673     o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
3674     o bug fix in find_alpha.F for MDJWF:
3675     - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
3676     change rho -> rho-rhoConst
3677     - replace call find_rho to find_rhonum
3678     o initialisation of rFlx extended to full array (required by TAF)
3679     and shifted to thermodynamics
3680     o removed PTRACERS.h in ptracers routine
3681     o added surfacetendencyPtr to S/R parameter list pracers_forcing
3682     o Correcting initialisations for fVerU, fVerV.
3683     o helping TAF to recognize dependency on kUp for
3684     fVerU, fVerV
3685     o Replacing delZ by delR in pkg/ctrl/
3686 jmc 1.1203 checkpoint51o_pre (2003/10/24)
3687 dimitri 1.192
3688 edhill 1.195 o undid all of cp51 pending some cleanups and discussion
3689 heimbach 1.197 o added the [#include "AD_CONFIG.h"] statement to all files that need
3690     it for adjoint/tl #defines
3691     o re-worked the build logic in genmake2 to support AD_CONFIG.h
3692     o removed tools/genmake since it no longer works
3693 dimitri 1.194
3694 jmc 1.1203 checkpoint51n_post (2003/10/23)
3695 dimitri 1.194 o modifications to make FREEZE flux visible to pkg/kpp
3696     - moved surfaceTendencyTice from pkg/seaice to main code
3697     - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
3698     - subroutine FREEZE now limits only surface temperature
3699     (this means new output.txt for global_ocean.90x40x15,
3700     global_ocean.cs32x15, and global_with_exf)
3701     o added surface flux output variables to TIMEAVE_STATVARS
3702    
3703 jmc 1.1203 checkpoint51n_pre (2003/10/23)
3704 dimitri 1.192 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
3705 edhill 1.193 o added [#include "AD_CONFIG.h"] to all files that use the following
3706     defines:
3707     - ALLOW_ADJOINT_RUN
3708     - ALLOW_TANGENTLINEAR_RUN
3709     - ALLOW_ECCO_OPTIMIZATION
3710 edhill 1.190
3711 jmc 1.1203 checkpoint51m_post (2003/10/21)
3712 edhill 1.190 o incorporating changes to get TAMC/TAF working in genmake2
3713     - added new TAMC/TAF targets to the Makefile
3714     - various cleanups related to package handling
3715 edhill 1.191 - these changes should have no impact on the forward model
3716 dimitri 1.189
3717 jmc 1.1203 checkpoint51l_post (2003/10/20)
3718 dimitri 1.189 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
3719     - faster algorithm for cal_addtime.F
3720     - higher precision arithmetic, where needed
3721     - pkg/exf *startdate variables changed from calendar date to
3722     model integration time
3723    
3724 jmc 1.1203 checkpoint51l_pre (2003/10/17)
3725 jmc 1.188 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
3726     o enable to apply restoring on S & T only in a latitude band.
3727     o update output (external_forcing_surf modif. change truncation errors)
3728     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
3729 edhill 1.186
3730 jmc 1.1203 checkpoint51k_post (2003/10/16)
3731 jmc 1.187 o change default to: useNHMTerms=.FALSE.
3732     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
3733     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
3734     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
3735     exp1, ideal_2D_oce
3736     - change data file of oceanic exp (leave the results unchanged for now)
3737     exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
3738     o set gravitySign automatically according to the vertical coordinate used
3739     (and change sign: back to "logical" value: +1 when R increases downward)
3740 edhill 1.186 o added an include barrier to the default CPP_OPTIONS.h and
3741     removed the #include "PACKAGES_CONFIG.h" from it
3742 jmc 1.187 o fix a bug in mom_fluxform (from chk51j_post)
3743 heimbach 1.185
3744 jmc 1.1203 checkpoint51j_post (2003/10/10)
3745 heimbach 1.185 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
3746     o adjusted some flow directives (dynamics, thermodynamics)
3747     o added cubed-sphere case to test cost function
3748     o heckpoint_lev?_directives.h now include
3749     pkg-specific directives, whenever those are enabled.
3750     o Moving pkg-specific flow directives to corresponding pkg
3751     Moving pkg-specific differentiation list to corresponding pkg
3752     Moving pkg-specific checkpoint-lev storing to corresponding pkg
3753     ---> conventions are
3754     - pkg_ad.flow
3755     - pkg_ad_diff.list
3756     - pkg_ad_check_lev?_dir.h
3757 stephd 1.181
3758 jmc 1.1203 checkpoint51i_post (2003/10/09)
3759 edhill 1.184 o merge of the branch-genmake2
3760     - knowingly breaks the older genmake
3761     - automatic generation of all ALLOW_${PKG_NAME} defines
3762     - new testreport supersedes older testscript
3763     o large number of package inclusion and header cleanups
3764 jmc 1.1203 checkpoint51i_pre (2003/10/08)
3765 edhill 1.184
3766 edhill 1.183 o new output for adjoin of global ocean vector invariant
3767     o fix for checkpoint of thermodynamic seaice and bulk_force
3768     o Steph gchem various cleanups
3769    
3770 stephd 1.181 checkpoint 51h_pre
3771 edhill 1.183 o fixed some single quotes
3772 stephd 1.181 o modify gchem pkg to be more versatile
3773     o modifications to clean up dic pkg
3774     o add pkg/cfc
3775 heimbach 1.182
3776 jmc 1.1203 checkpoint51g_post (2003/10/02)
3777 heimbach 1.182 o provide links for ARPACK and ADM*TLM
3778     o start removing verification/vero/
3779     o update AD-related stuff
3780     (in particular some IF-statements in model/src/ routines)
3781     o adding to verification/global_ocean.90x40x15/ adjoint of
3782     vector invariant setup
3783 dimitri 1.177
3784 jmc 1.1203 checkpoint51f_post (2003/10/02)
3785 jmc 1.179 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
3786 dimitri 1.178 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
3787 dimitri 1.177 of tracer Green's fucntions for ocean inversion project.
3788 dimitri 1.175
3789 jmc 1.1203 checkpoint51f_pre (2003/08/07)
3790 dimitri 1.175 o Added on-the-fly spatial interpolation capability
3791     "USE_EXF_INTERPOLATION" to pkg/exf.
3792 dimitri 1.176 - This is a temporary Cartesian-grid hack until
3793 dimitri 1.175 the super-duper ESMF coupler becomes available.
3794 dimitri 1.176 - See verification/global_with_exf/README for usage example.
3795     - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
3796     flags and modified pkg/seaice accordingly.
3797 dimitri 1.175 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
3798     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
3799     non-local transport term.
3800 heimbach 1.172
3801 jmc 1.1203 checkpoint51e_post (2003/08/03)
3802 jmc 1.174 o pkg/mom_vecinv:
3803     - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
3804     - add time-ave diagnostic of vorticity advection.
3805     o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
3806     o atmospheric geopotential: - include water vapor effect;
3807     - use p^kappa in p* scaling.
3808 jmc 1.173 o land pkg: read initial state from files.
3809     o AIM : add stratospheric drag in the upper level
3810    
3811 jmc 1.1203 checkpoint51d_post (2003/07/18)
3812 jmc 1.173 o change function ILNBLNK (=> last non-blank char.) to return zero
3813     (instead of the string length) when the string. char is empty
3814 jmc 1.171 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
3815 heimbach 1.172 o modif's to restore TAMC compatibility
3816     - avoid "_d" constructs in PARAMETER declarations
3817     - avoid interrupting lines by comment lines
3818     o Use cluster local disks for purely local I/O
3819     vs. globally visible disks needed for ctrl stuff
3820     (merged from ecco-branch)
3821     - new active_file_loc... and mdsio_..._loc routines
3822     - affected packages: autodiff, ctrl, grdchk, mdsio
3823 heimbach 1.169
3824 jmc 1.1203 checkpoint51c_post (2003/07/08)
3825 heimbach 1.170 o introducing integer flag debugLevel
3826     - debLevZero: suppress all output
3827     - debLevA: standard
3828     - debLevB: equivalent to current debugMode=.TRUE.
3829     o introducing pathname variable mdsioLocalDir for mdsio
3830     that can be specified at runtime
3831     (relevant for cluster I/O to local disk)
3832     `
3833 heimbach 1.169 >>>checkpoint51b_post
3834     adjoint of ptracers
3835     o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
3836     o extended state in checkpoint_lev?, etc.
3837     o alternative ctrl/cost with tr1 or ptracer
3838     o new comlev1_bibj_ptracers
3839     o new ptracers.flow
3840     o made ptracers_forcing same as external_forcing_s
3841     o added verification for adjoint with ptracers
3842     - adm. grdchk fail so far
3843     - tlm. grdchk OK
3844     - checked tapelev/comlev recomputations: OK
3845     <<<checkpoint51b_pre
3846 stephd 1.168
3847 jmc 1.1203 checkpoint51a_post (2003/06/25)
3848 stephd 1.168 o added code for biogeochemistry package
3849     - new pkgs: dic, gchem
3850     - new subroutine in ptracers
3851     o modify code for biogeo packages
3852     - in model/src and pkg/ptracers
3853 heimbach 1.166
3854 jmc 1.1203 checkpoint51 (2003/06/24)
3855 heimbach 1.166 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
3856     - autodiff, ctrl, exf, grdchk, seaice
3857     kept separate packages
3858     - cost, ecco, obcs
3859 heimbach 1.167 o updating verification/internal_wave, verification/lab_sea
3860     (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
3861 heimbach 1.165
3862 jmc 1.1203 checkpoint50i_post (2003/06/23)
3863 heimbach 1.165 o Preparing next differentiable checkpoint and sync
3864     of MAIN vs. ecco-branch
3865     - 1st step: this one is differentiable
3866     - 2nd step: next(! not this) checkpoint will have updated packages
3867     from ecco-branch)
3868 jmc 1.161
3869 jmc 1.1203 checkpoint50h_post (2003/06/20)
3870 jmc 1.163 o new package "land": provide surface BC for AIM.
3871     o pkg/ptracers: apply exchange to all tracers after reading a pickup.
3872 jmc 1.161 o AIM: use true log-P extrapolation for near surface temp (= as in
3873     F.Molteni paper) ; update aim.5l_cs output.
3874 adcroft 1.162 o New variable in PARM03 for more flexible pickups
3875 heimbach 1.164 o somewhat cleaned package initialisation sequence for
3876     ctrl/ cost/ ecco/ in packages_... routines
3877 dimitri 1.160
3878 jmc 1.1203 checkpoint50g_post (2003/05/23)
3879 dimitri 1.160 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
3880     - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
3881     - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
3882     made the default because of faster convergence than ADI
3883 heimbach 1.159
3884 jmc 1.1203 checkpoint50f_post (2003/05/23)
3885 heimbach 1.159 o exf totally restructured
3886     - replaced all exf_set_ routines by one generic exf_set_gen.F
3887     and made sure it's still differentiable
3888     - split exf_getffields.F into new exf_bulkformulae.F
3889     - exf_inscal_/exf_outscal_ suffixes consistent with field names
3890     - updated adjoint/makefile and relevant verif. accordingly
3891 adcroft 1.156
3892 jmc 1.1203 checkpoint50f_pre (2003/05/23)
3893 jmc 1.157 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
3894     + change Evap over land. (update aim.5l_cs output)
3895 adcroft 1.156 o added missing .cvsignores and made uniform across expts
3896     o changed configuration of tidal_basin_2d expt
3897     o added pkg/debug functions for tracing code in fatal crashes
3898     o tidied pkg/monitor to use MONITOR_OPTIONS.h
3899     o new fn in pkg/monitor to stop model if solution grows too big
3900     o removed lots of single quotes from comments
3901    
3902 jmc 1.1203 checkpoint50e_post (2003/05/14)
3903 mlosch 1.155 o make KPP work with PTRACERS
3904     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
3905     nearly a copy of kpp_transport_s
3906     - there is no analogue to SurfaceTendencyS, so I have to use
3907     gPtr(of the surface layer) instead
3908     o add a new platform SunFire+mpi (SunFire 15000) to genmake
3909 jmc 1.1203 checkpoint50e_pre (2003/05/13)
3910 mlosch 1.155
3911 jmc 1.1203 checkpoint50d_post (2003/05/13)
3912 mlosch 1.154 o change kpp output from multiple-record state files to single-record state
3913     files analogous to write_state.F
3914     o reduce the output frequency of cg3d-related stuff to the monitor frequency,
3915     analogous to the cg2d-related output.
3916 mlosch 1.155 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
3917     so that writing to internal file fn (with length 512) fails.
3918 jmc 1.1203 checkpoint50d_pre (2003/05/12)
3919 jmc 1.151
3920 jmc 1.1203 checkpoint50c_post (2003/05/12)
3921 jmc 1.153 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
3922 jmc 1.152 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
3923 jmc 1.151 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
3924     o bug fixed in convective adjustment diagnostic (multi-tile set-up).
3925     o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
3926 dimitri 1.150
3927 jmc 1.1203 checkpoint50c_pre (2003/04/30)
3928 dimitri 1.150 Merging from release1_p13:
3929     o bug fix for pkg/seaice dynamic solver
3930     o Added SEAICE_initialHEFF to pkg/seaice
3931 jmc 1.149
3932 jmc 1.1203 checkpoint50b_post (2003/04/17)
3933 jmc 1.149 o store u*,v* in gU,V instead of in guNm1,gvNm1
3934     o in order to put the momForcing out of the Adams-Bashforth:
3935     move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
3936     to timestep.F
3937     o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
3938     o re-generate output for highly sensitive test-exp:
3939     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
3940 heimbach 1.146
3941 jmc 1.1203 checkpoint50b_pre (2003/04/17)
3942 jmc 1.147 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
3943 heimbach 1.146 o corrected CPP option mismatch in exf_Bulk... functions for case
3944     #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
3945 heimbach 1.145
3946 jmc 1.1203 checkpoint50a_post (2003/03/21)
3947 heimbach 1.145 o Bug fix for merging between c50 and KPP.
3948     ikey was passed from thermodynamics to kpp_calc via
3949     common block rather than being recomputed in kpp_calc,
3950     in contradiction with new key itdkey.
3951     New key ikppkey created, and tamc.h headers updated.
3952 heimbach 1.143
3953 jmc 1.1203 checkpoint50 (2003/03/08)
3954 heimbach 1.144 - 2nd step of merge with ecco-branch:
3955     merge changes in ecco-branch back into main trunk
3956     - bug fix in find_alpha
3957     - more storing in gmredi_calc_tensor.F, kpp_routines.F
3958     - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
3959     - merged some sliced AD support routines
3960    
3961 jmc 1.1203 checkpoint49 (2003/03/06)
3962 heimbach 1.143 merged from ecco-branch:
3963     o exf:
3964     - Enable initialisation of forcing fields to constant
3965     (runtime) values.
3966     - in exf_getffields.F
3967     Reduce i-/j-loop to interior domain, discarding overlaps.
3968     That also fixes wrong TAF-key computations for key_1, key_2
3969     with bulf formulae.
3970     - exf_init.F modify #ifdef for exf_init_evap
3971     - exf_getffieldrec.F, ctrl_getrec.F
3972     The following INT-usages are not safe:
3973     fldsecs = int(fldsecs/fldperiod)*fldperiod
3974     fldcount = int(fldsecs/fldperiod) + 1
3975     and were modified.
3976     o autodiff: checkpoint_lev...
3977     - updated storing for bulk formulae (some arrays were missing)
3978     - added state for seaice package
3979     - synchronized with main branch
3980     o DIVA:
3981     Modif.s in
3982 heimbach 1.144 - the_main_loop.F
3983     - the_model_main.F
3984 heimbach 1.143 and added cost_final_restore.F cost_final_store.F
3985     o With these changes, it is possible to fully separate
3986     the first forward run to compute the cost function (mdthe_main_loop)
3987     and adjoint runs over individual DIVA intervals (adthe_main_loop)
3988     into separate model executions.
3989     This enables better tuning of DIVA to given queue sizes.
3990     o Loss of cost function value in consecutive DIVA runs is
3991     fixed by storing to 'costfinal' file.
3992     o Appropriate call of ctrl_unpack/_pack,grdchk_main at
3993     beginning/end of adjoint integration is accounted for.
3994     The current changes apply to TAF-1.4.26.
3995     TAF has one remaining bug, requiring one manual change
3996     (see MITgcm manual).
3997     o cal: synchronized between MAIN and ecco-branch
3998 heimbach 1.141
3999 jmc 1.1203 checkpoint48i_post (2003/03/05)
4000 heimbach 1.141 o Changes to restore differentiability of code w.r.t. previous tag
4001     (mostly adding new routines to make list and replacing
4002     pressure by totPhiHyd).
4003     o Updated and merged grdchk package
4004     - has both ADM and TLM checks
4005     - works for single- and multi-proc.
4006     - output cleaned
4007     - worked successfully for parallel DIVA
4008     o genmake:
4009     - Adding -platform=SP4
4010     - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
4011     o Modif. for DIVA:
4012     ctrl_unpack should not be called in intermediate DIVA interval.
4013     (similar thing would apply for active files such as
4014     tbar, sbar, psbar, which should not be reinitialised;
4015     only relevant for ecco-branch)
4016 dimitri 1.136
4017 jmc 1.1203 checkpoint48h_post (2003/02/28)
4018 jmc 1.137 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
4019 dimitri 1.136 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
4020     o Added SEAICE_initialHEFF to pkg/seaice
4021 dimitri 1.139 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
4022 jmc 1.135
4023 jmc 1.1203 checkpoint48g_post (2003/02/18)
4024 jmc 1.135 --- EOS:
4025     o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
4026     store total Potential in totPhyHyd for diagnostics & EOS.
4027     o fix restart and overlap Pb when using Z-coord and EOS funct. of P
4028     --- Pressure/geopotential gradient:
4029     o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
4030     o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
4031     ( changes results of global_ocean_pressure )
4032     o NLFS + z-coord.: add eta*Rho' contribution.
4033     o accurate phiHyd when using interface-W at the middle between 2 centers
4034     ( changes results of ideal_2D_oce )
4035     o includes r* 2nd term in potential gradient.
4036 dimitri 1.134
4037 jmc 1.1203 checkpoint48f_post (2003/02/18)
4038 dimitri 1.134 Merging from release1_p12:
4039     o Modifications for using pkg/exf with pkg/seaice
4040     - improved description of the various forcing configurations
4041     - added basic radiation bulk formulae to pkg/exf
4042     - units/sign fix for evap computation in exf_getffields.F
4043     - updated verification/global_with_exf/results/output.txt
4044     o Added pkg/sbo for computing IERS Special Bureau for the Oceans
4045     (SBO) core products, including oceanic mass, center-of-mass,
4046     angular, and bottom pressure (see pkg/sbo/README.sbo).
4047     o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
4048     to avoid negative values in shallow regions.
4049     - updated verification/natl_box/results/output.txt
4050     - updated verification/lab_sea/results/output.txt
4051     o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
4052     o Added useSingleCpuIO option (see PARAMS.h).
4053     o Updated useSingleCpuIO option in mdsio_writefield.F to
4054     work with multi-field files, e.g., for single-file pickup.
4055     o pkg/seaice:
4056     - bug fix in growth.F: QNET for no shortwave case
4057     - added HeffFile for specifying initial sea-ice thickness
4058     - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
4059     o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
4060     kpp_transport_t.F, forward_step.F, and the_main_loop.F
4061     o pkg/seaice:
4062     - adjoint-friendly modifications
4063     - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
4064 jmc 1.131
4065 jmc 1.1203 checkpoint48e_post (2003/02/12)
4066 jmc 1.131 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
4067 jmc 1.132 o dynamics: change definition of computational domain & adapt mom_fluxform
4068     accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
4069     o following exp works with Olx=Oly=2 (and pass through checkbounds option):
4070     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
4071 jmc 1.133 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
4072 jmc 1.132 global_ocean.90x40x15 global_with_exf global_ocean_pressure
4073     inverted_barometer solid-body.cs-32x32x1
4074     (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
4075 jmc 1.130
4076 jmc 1.1203 checkpoint48d_post (2003/02/09)
4077 jmc 1.130 o in preparation for r*:
4078     a) use pre-computed gradient of hydrostatic potential:
4079     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
4080     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
4081     => affects results of glob_oce_pressure (different truncation error)
4082     update output.txt of ideal_2D_oce & global_ocean_pressure
4083 jmc 1.129
4084 jmc 1.1203 checkpoint48d_pre (2003/02/08)
4085 jmc 1.129 o in preparation for r*:
4086     new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
4087     pass the 2 comp. of the grad. as arguments to momentum S/R.
4088     but for the moment, only used if it does not change the results.
4089     o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
4090 jmc 1.126
4091 jmc 1.1203 checkpoint48c_post (2003/02/06)
4092 heimbach 1.128 Modifications in treatment of initial flux forcing controls
4093     to avoid extra storing of flux fields.
4094    
4095 jmc 1.1203 checkpoint48c_pre (2003/01/21)
4096 adcroft 1.127 o Added tidal_basin_2d experiment (currently 1D!)
4097 jmc 1.126 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
4098 jmc 1.124
4099 jmc 1.1203 checkpoint48b_post (2003/01/27)
4100 jmc 1.124 o r* coordinate added in #ifdef NONLIN_FRSURF block.
4101     (modification to pressure gradient not yet implemented)
4102     o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
4103     (for U & V) that are used for vertical advection of momentum.
4104 jmc 1.123
4105 jmc 1.1203 checkpoint48a_post (2003/01/24)
4106 jmc 1.123 o In preparation for r*, use temp. array to compute vertical transport
4107     in flux-form momentum pkg. => change results of few test-exp.
4108     Update output of: exp4, exp5, front_relax, global_ocean_pressure,
4109     lab_sea, natl_box & plume_on_slope
4110 jmc 1.122
4111 jmc 1.1203 checkpoint48 (2003/01/23)
4112 jmc 1.122 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
4113 heimbach 1.121
4114 jmc 1.1203 checkpoint47j_post (2003/01/21)
4115 jmc 1.120 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
4116 heimbach 1.121 o moved adexch from forward_step to addummy_in_stepping
4117     o added exch in ctrl_map_...
4118     o aveFreq.=0. at end of cost_final to avoid overwrite in
4119     reverse checkpointing loop
4120     o Yet more changes in gmredi:
4121     * adgmredi_calc_tensor
4122     avoiding all recomputation of gmredi_slope_limit
4123     * adgmredi_x/y/rtransport
4124     added flag for excessive storing to avoid recomp. of
4125     u/v/rtans, dTdx/y/z
4126     -> this is not really necessary and very memory-consuming
4127     * adgmredi_slope_psi:
4128     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
4129     * gmredi_slope_limit
4130     re-activated full calculation of taperfct for case 'ac02'
4131     o updating verification/ adjoints of carbon, global_ocean.90x40x15
4132 heimbach 1.116
4133 jmc 1.1203 checkpoint47i_post (2003/01/13)
4134 jmc 1.119 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
4135     o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
4136     default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
4137     o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
4138     o gmredi: fix few bugs.
4139    
4140 adcroft 1.118 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
4141 heimbach 1.116 This will be a good checkpoint to plug into the ecco-branch.
4142     o few modif.'s to get latest version adjointed
4143     (mainly kick out code in ini_linear_phisurf)
4144     o modif's to run adjoint with exactConserv
4145     o case GM_BOLUS_ADVEC should be cleaned
4146     S/R gmredi_slope_psi should be cleaned
4147     o verification/carbon now has exactConserv=.TRUE.
4148 jmc 1.114
4149 jmc 1.1203 checkpoint47g_post (2003/01/10)
4150 jmc 1.114 o time-average AIM output: becomes independent from statvars time-average
4151     (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
4152 heimbach 1.115 o After TAF bug fix:
4153     Tested adjoint of gmredi package.
4154     Tests were done with checkpoint47 rather than with latest
4155     checkpoint47f_post since the latter is broken for the adjoint
4156     verification/carbon/ contains both ADM and TLM gradient checks.
4157     Here they are, before they get changed/lost/stolen.
4158     Mostly modif.'s to fix numerical sensitivities.
4159     Gradient checks OK for
4160     - GM_taper_scheme:
4161     * clipping
4162     * ac02
4163     * linear
4164     * glw91
4165     * dm95
4166     * ldd97
4167     - GMREDI_OPTIONS:
4168     * GM_VISBECK_VARIABLE_K
4169     * GM_NON_UNITY_DIAGONAL
4170     * GM_EXTRA_DIAGONAL
4171     * GM_BOLUS_ADVEC
4172     in conjunction with data.gmredi parameters to be checked in
4173     in a few minutes under verification/carbon/code/
4174 cheisey 1.112
4175 jmc 1.1203 checkpoint47f_post (2002/12/28)
4176 dimitri 1.113 Merging from release1_p10:
4177     o modifications for using pkg/exf with pkg/seaice
4178     - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
4179     and SEAICE_EXTERNAL_FLUXES
4180     - pkg/exf CPP options EXF_READ_EVAP and
4181     EXF_NO_BULK_COMPUTATIONS
4182     - usage examples are Experiments 8 and 9 in
4183     verification/lab_sea/README
4184     - verification/lab_sea default experiment now uses
4185     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
4186    
4187 jmc 1.1203 checkpoint47e_post (2002/12/27)
4188 cheisey 1.112 o created a tag prior to creating a branch
4189    
4190 jmc 1.1203 checkpoint47d_post (2002/12/16)
4191 mlosch 1.111 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
4192     at the bottom boundary had an erroneous half slip boundary condition
4193     o added bottom drag and no slip boundary condition capabilities to
4194     oceanic pressure coordinates code
4195     o added new verification experiment global_ocean_pressure, this experiment is
4196     also described in the tutorial section of the manual
4197 jmc 1.1203 checkpoint47d_pre (2002/12/16)
4198 cheisey 1.110
4199 jmc 1.1203 checkpoint47c_post (2002/12/16)
4200 cheisey 1.110 o Added a verification experiment for a global cubed-sphere ocean run
4201     - verification/global_ocean.cubed32x32x30
4202     - uses pkg/therm_seaice and pkg/bulk_forcing
4203 jmc 1.109
4204     o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
4205     o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
4206     when using P-coordinate; only implemented for atmospheric config.
4207     o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
4208     NOTES: requires option NONLIN_FRSURF to be "#define".
4209     o update advect_xz/results/output.txt (left from checkpoint44g_post)
4210 dimitri 1.108
4211 jmc 1.1203 checkpoint47b_post (2002/12/05)
4212 dimitri 1.108 Merging from release1_p9:
4213     o pkg/seaice
4214     - removed GOTO's and added taf directives
4215     - double precision constants to reduce the g77 (Linux)
4216     to F77 (SGI) differences reported in release1_p8
4217     o tools/genmake
4218     - added SGI options
4219     o verification/testscript
4220     - updated to that of checkpoint47a_post
4221     o verification/global_ocean.90x40x15/input/eedata
4222     - modified for SGI f77 compatibility
4223     o verification/lab_sea
4224     - added description of sea-ice model
4225     - added missing matlab routines
4226     - added test of thermodynamics parallelization
4227 jmc 1.105
4228 jmc 1.1203 checkpoint47a_post (2002/11/23)
4229 jmc 1.105 o new pkg: aim_v23
4230     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
4231     for now, keep the same surface forcing as before.
4232     - Part-Cell implemented into AIM; check that Heat & Water are conserved
4233     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
4234     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
4235     o add diagnostic of surface correction term in monitor output
4236 jmc 1.106
4237     o bulk_force and therm_seaice
4238 cheisey 1.107 - Two packages: bulk_force (Bulk forcing)
4239     and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
4240     - Earlier integration from Stephaine Dutkiewicz
4241     and Patrick Heimbach.
4242     - Two ifdef statements for compile time,
4243     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
4244 heimbach 1.104
4245 jmc 1.1203 checkpoint47 (2002/11/15)
4246 heimbach 1.104 differentiable version of checkpoint46n_post
4247     o bug fix in quasihydrostaticterms
4248     o * "clean" adjoint code (in terms of extensive recomputations)
4249     can now be obtained for all GMREDI options (i.e. for
4250     - GM_VISBECK_VARIABLE_K
4251     - GM_NON_UNITY_DIAGONAL
4252     - GM_EXTRA_DIAGONAL
4253     - GM_BOLUS_ADVEC )
4254     * However, wrong gradient check problem remains unsolved.
4255     * New CPP options have been introduced for different
4256     tapering schemes
4257     o external_fields_load now part of differentiation list
4258     o pressure needs multiple storing;
4259     would be nice to have store_pressure at beginning or
4260     end of forward_step, e.g. by having phiHyd global (5-dim.)
4261     (NB: pressure is needed for certain cases in find_rho,
4262     which is also invoked through convective_adjustment).
4263     o recomputations in find_rho for cases
4264     'JMD95'/'UNESCO' or 'MDJWF' are OK.
4265     o #define ATMOSPHERIC_LOADING should be differentiable
4266     o ini_forcing shifted to begining of initialise_varia
4267     o Incorporating QNVS line search routines into MITgcm
4268     (this is separate code, and therefore not under pkg)
4269     lsopt/, optim/
4270     o Updated verification/carbon/
4271     - #define GM_VISBECK_VARIABLE_K
4272     - GM_taper_scheme = 'ldd97'
4273 heimbach 1.103
4274 jmc 1.1203 checkpoint46n_post (2002/11/12)
4275 heimbach 1.103 Merging from release1_p8:
4276     o verification/natl_box:
4277     updating new external_fields_load routine
4278     o New package: pkg/seaice
4279     Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
4280     The sea-ice code is based on Hibler (1979-1980).
4281     Two sea-ice dynamic solvers, ADI and LSR, are included.
4282     In addition to computing prognostic sea-ice variables and diagnosing
4283     the forcing/external data fields that drive the ocean model,
4284     SEAICE_MODEL also sets theta to the freezing point under sea-ice.
4285     The implied surface heat flux is then stored in variable
4286     surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
4287     kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
4288     non-local transport term. Because this call precedes model
4289     thermodynamics, temperature under sea-ice may not be "exactly" at
4290     the freezing point by the time theta is dumped or time-averaged.
4291     N.B.: fairly large differences in accuracy occur across
4292     different platforms/compilers; comparison between
4293     g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
4294     generated output gives:
4295     T S U V
4296     C D M c m s m s m s m s
4297     n p a R g m m e . m m e . m m e . m m e .
4298     f n k u 2 i a a d i a a d i a a d i a a d
4299     g d e n d n x n . n x n . n x n . n x n .
4300    
4301     Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
4302     o GAD:
4303     - generated new common blocks to account for call of
4304     same gad routines with differing traceridentities
4305     (needed to modify tracerIdentity indices in GAD.h)
4306     - generated separate common blocks for case useCubedSphereExchange
4307     (Department of Futurology)
4308     - parameter lists to gmredi_?transport: added tracerIdentity
4309     - added new key indices to tamc.h
4310     o external_fields_load:
4311     - added this routine to TAF list
4312     - needed to make some common blocks global and additional storing
4313     along the same lines as exf package (checkpoint_lev?_directives.h)
4314     o exf:
4315     updated external forcing package
4316     - bug fixes carried over from ecco-branch
4317     (missing OBCS_OPTIONS.h in two routines)
4318     - enable easy to use "no forcing".
4319     - added exf I/O for atmospheric loading
4320     - added exf I/O for runoff data
4321     - transfered scaling between exf <-> MITgcm to exf namelist
4322     o Adding new verification experiment global_with_exf.
4323     This verification experiment is almost identical to the
4324     global_ocean.90x40x15 experiment, except that it uses
4325     the exf (and cal) package instead of the
4326     external_fields_load routine (cf README file).
4327 adcroft 1.94
4328 jmc 1.1203 checkpoint46m_post (2002/11/07)
4329 adcroft 1.101 o modified testscript to return -- when there are no lines of "%MON" output
4330 adcroft 1.100 o added new flag "quasiHydrostatic" for QH mode
4331     and new routine quasihydrostaticterms()
4332 adcroft 1.99 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
4333     New routine: mom_u_coriolis_nh()
4334 adcroft 1.98 o fixed sign of non-hydrostatic metric terms in u and v equations.
4335     Depend on correct sign of gravitySign.
4336 adcroft 1.97 o added work.pc* to .cvsignore in aim directories using ifc
4337 adcroft 1.96 o introduced flag for controllin non-hydrostatic metric terms
4338 adcroft 1.95 o removed gravitySign from PARM04
4339 adcroft 1.94 o switched to g77/ifc from pgf77 in aim experiments
4340 mlosch 1.93
4341 jmc 1.1203 checkpoint46l_post (2002/11/01)
4342 mlosch 1.93 o made convective adjustment work with pressure coordinates:
4343     - changed the direction of k-loop in convective_adjustment.F for the
4344     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
4345     - adjusted the reference pressure k-index in convective_adjustment.F
4346     - adjusted the convection condition in convect.F (in analogy to
4347     calc_ivdc.F)
4348     - convective_adjustment no longer computes anything on the halos
4349     - removed the warnings about negative salinity from find_rho.F and
4350     find_alpha.F; instead the new routine look_for_neg_salinity, called
4351     at the beginning of find_rho, find_alpha, and find_beta, does a
4352     check of the entire slice, if CPP-option
4353     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
4354 jmc 1.1203 checkpoint46l_pre (2002/10/23)
4355 mlosch 1.91
4356 jmc 1.1203 checkpoint46k_post (2002/10/23)
4357 mlosch 1.91 o fixed the verification/global_ocean.90x40x15 experiment:
4358     - new bathymetry (the world according to A., JMC, and M.)
4359     - new initial fields and forcing fields (*.bin files)
4360     - new POLY3.COEFFS (for the next release one should switch to a full
4361     equation of state: JMD95P or MDJWF)
4362     - fixed several errors and redundancies in the data file
4363     - experiment uses looped cells
4364     - added matlab directory with diagnostic scripts for plotting of output
4365 jmc 1.90
4366     o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
4367     - read AIM physics parameters from a file (data.aimphys)
4368     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
4369 jmc 1.89
4370 jmc 1.1203 checkpoint46j_post (2002/10/07)
4371 jmc 1.89 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
4372     o move wVel computation at the end of the time step, in S/R integr_continuity
4373     o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
4374     o update timeave pkg for wVel diagnostic.
4375 jmc 1.1203 checkpoint46j_pre (2002/09/27)
4376 mlosch 1.87
4377 jmc 1.1203 checkpoint46i_post (2002/09/25)
4378 jmc 1.88 o Clean up AIM package (and keep the results unchanged):
4379     include CPP_OPTION and use IMPLICT NONE in all routines ;
4380     declare all the variables _RL ; use _d 0 for all numerical constants.
4381     use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
4382 mlosch 1.87
4383 jmc 1.1203 checkpoint46h_post (2002/09/25)
4384 mlosch 1.87 o cleaned up the use of rhoNil and rhoConst.
4385     - rhoNil should only appear in the LINEAR equation of state, everywhere
4386     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
4387     and the dynamical equations are all divided by rhoConst
4388     o introduced new parameter rhoConstFresh, a reference density of fresh
4389     water, to remove the fresh water flux's dependence on rhoNil. The default
4390     value is 999.8 kg/m^3
4391     o cleanup up external_forcing.F and external_forcing_surf.F
4392     - can now be used by both OCEANIC and OCEANICP
4393 jmc 1.1203 checkpoint46h_pre (2002/09/18)
4394 mlosch 1.87
4395     Added code to convert surface volume flux (fresh water) into
4396     a mass flux when using P coordinates in the ocean (OCEANICP).
4397     Note: It assumes you have set rho0=rhoConst=density of fresh water.
4398 mlosch 1.86
4399 jmc 1.1203 checkpoint46g_post (2002/09/18)
4400 mlosch 1.86 o Include a new diagnostic variable phiHydLow for the ocean model
4401     - in z-coordinates, it is the bottom pressure anomaly
4402     - in p-coordinates, it is the sea surface elevation
4403     - in both cases, these variable have global drift, reflecting the mass
4404     drift in z-coordinates and the volume drift in p-coordinates
4405     - included time averaging for phiHydLow, be aware of the drift!
4406     o depth-dependent computation of Bo_surf for pressure coordinates
4407     in the ocean (buoyancyRelation='OCEANICP')
4408     - requires a new routine (FIND_RHO_SCALAR) to compute density with only
4409     Theta, Salinity, and Pressure in the parameter list. This routine is
4410     presently contained in find_rho.F. This routine does not give the
4411     correct density for 'POLY3', which would be a z-dependent reference
4412     density.
4413     o cleaned up find_rho
4414     - removed obsolete 'eqn' from the parameter list.
4415     o added two new verification experiments: gop and goz
4416     (4x4 degree global ocean, 15 layers in pressure and height coordinates)
4417 jmc 1.1203 checkpoint46g_pre (2002/09/16)
4418 heimbach 1.85
4419 jmc 1.1203 checkpoint46f_post (2002/09/16)
4420 heimbach 1.85 o Enable tangent linear (forward mode) gradient checks:
4421     - extended active file handling to g_... files
4422     - added TANGENT_SIMULATION to theSimulationMode
4423     - extended grdchk package accordingly
4424     o added tangent linear setup in verification/carbon/code_ftl
4425     o added adjoint setup in verification/front_relax/code_ad
4426 mlosch 1.82
4427 jmc 1.1203 checkpoint46e_post (2002/09/05)
4428 mlosch 1.83 o Added new equation of state -> MDJWF
4429     - EOS of McDougall et al., 2002, JAOT, submitted
4430     - caveat: the equation of state is only valid for a smaller (more
4431     realistic?) range of values than JMD95P/Z and UNESCO
4432     - added masks to the calculation of pressure in store_pressure
4433     - added more check values for density in check_eos (ini_eos.F), some of
4434     the old check values are out of the range of the MDJWF-eos, so don't
4435     expect perfect matches for those
4436 jmc 1.1203 checkpoint46e_pre (2002/08/19)
4437 mlosch 1.83
4438 jmc 1.1203 checkpoint46d_post (2002/08/19)
4439 mlosch 1.82 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
4440     'OCEANICP', also initialised field pressure correctly in ini_eos in the
4441     case of pressure coordinates. eosType='JMD95Z' in
4442     combination with buoyancyRelation='OCEANICP' now causes an error.
4443     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
4444     in find_alpha/beta.
4445 jmc 1.1203 checkpoint46d_pre (2002/08/15)
4446 mlosch 1.82
4447     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
4448     so that JMD95Z and JMD95P give approptiate static stability in find_rho.
4449 adcroft 1.81
4450 jmc 1.1203 checkpoint46c_post (2002/08/15)
4451 adcroft 1.81 o Changes necessary for ocean in p-coordinates
4452     - Added new buoyancy relation = 'OCEANICP'
4453     - Added new parameters = gravitySign (this used to be contained inside
4454     the factor dRdZ which I added when we first switched to R coordinates).
4455     X GM/Redi is not compatible (yet)
4456     X bottom drag and no-slip need to be debugged.
4457 jmc 1.1203 checkpoint46c_pre (2002/08/07)
4458 mlosch 1.80
4459 jmc 1.1203 checkpoint46b_post (2002/08/07)
4460 mlosch 1.80 o Added new equation of state -> JMD95Z and JMD95P
4461 mlosch 1.83 - EOS of Jackett and McDougall, 1995, JAOT
4462 mlosch 1.80 - moved all EOS parameters into EOS.h
4463     - new routines ini_eos.F, store_pressure.F
4464     o Added UNESCO EOS, but not recommended because it requires
4465     in-situ temperature (see JMD95)
4466     o Modified formatting for knudsen2.f in utils/knudsen2 and added
4467     unesco.f to be used with POLY3
4468 jmc 1.1203 checkpoint46b_pre (2002/07/31)
4469 mlosch 1.79
4470 jmc 1.1203 checkpoint46a_post (2002/07/31)
4471 mlosch 1.79 o Added (atmospheric) pressure loading
4472     - new field in FFIELDS.h, etc...
4473     - new cpp flag ATMOSPHERIC_LOADING
4474     o Changed hFacC to _hFacC in calc_phi_hyd.F
4475     o Added SHORTWAVE_HEATING to some files for consistency
4476 jmc 1.1203 checkpoint46a_pre (2002/07/13)
4477 heimbach 1.78
4478 jmc 1.1203 checkpoint46 (2002/07/13)
4479 heimbach 1.78 further merges from release1_p5
4480     o new ctrl package
4481     - adopted from ECCO environment to enable optimization
4482     - added Eliassen Palm fluxes to controls
4483     o added Eliassen Palm flux controls to gradient check package
4484     o cost package
4485     - Compatible with new ctrl package
4486     - added Eliassen Palm cost hooks
4487     - modif's of existing cost functions
4488     o Adjoint-related bug fixes in kpp:
4489     - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
4490     - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
4491     o autodiff package
4492     - flow directives:
4493     + new for S/R do_the_model_io
4494     + enhanced for S/R checkpoint
4495     + new gmredi.flow
4496     - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
4497     disable adcommon.h/g_common.h by default.
4498     - fixed problem for adjoint of global_max
4499     o modified verification/carbon/
4500     o New setup for adjoint of global_ocean
4501     o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
4502     o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
4503     o incorporated hooks for sponge layer code (external_forcing.F)
4504    
4505 jmc 1.1203 checkpoint45d_post (2002/07/12)
4506 jmc 1.77 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
4507 jmc 1.76 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
4508     (affects plume_on_slope "cg2d" output)
4509 jmc 1.77 o add new parameter deltaTfreesurf for free-surface time stepping
4510     o exchange gT,gS when using staggerTimeStep & GM & Oly<4
4511 jmc 1.75 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
4512 jmc 1.74 o change phiMin in exp1 (to agree with documentation)
4513     o add new flags:
4514     - T,S forcing inside/outside Adams-Bashforth
4515     - turn off temp,salt advection and/or forcing
4516     - for each tracer, define internal flag for multiDimAdvection & A-B
4517     o monitor: change definition of KE to check conservation of Energy
4518 heimbach 1.73
4519 jmc 1.1203 checkpoint45c_post (2002/05/30)
4520 heimbach 1.73 o Removed f90 comments ("!")
4521     o Modified initialisations to enable exf package for MITgcm
4522     (without invoking ECCO_PACKAGE).
4523     o modifications to gradient check package (Martin Losch)
4524     - enable centered differences
4525     - modified format of standard output
4526 heimbach 1.72
4527 jmc 1.1203 checkpoint45b_post (2002/05/30)
4528 heimbach 1.72 o cleaned exchange calls in cg2d
4529     o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
4530     o included CPP option SINGLE_LAYER_MODE in thermodynamics
4531     to configure barotropic setup (Martin Losch)
4532     o moved some initialisations within bi,bj loop in dynamics
4533     (TAF flow dependency)
4534     o in initialise_varia, moved call packages_init_variables
4535     before convective_adjustment_init
4536     (corresponding adjustment of TAF tape initialisation).
4537     o in calc_diffusivity/calc_viscosity extended domain to full overlap.
4538 jmc 1.70
4539 jmc 1.1203 checkpoint45a_post (2002/05/01)
4540 jmc 1.71 o compute Rho over the whole domain (extend iMin,jMin indices)
4541     o specific exchange for X-slice domain (case Ny=1)
4542 jmc 1.70 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
4543     o solve_for_pressure : set cg2d_x to zero where OBCS are applied
4544 jmc 1.67
4545 heimbach 1.69 checkpoint44h_post = checkpoint45
4546     o Fix to restore differentiability:
4547     place at which packages_init_variables is called in
4548     initialise_varia is crucial for reverse control flow.
4549     o modifications in GMRedi to enable stable adjoint
4550     (corresponding modif's in thermodynamics, dynamics)
4551     o added missing hook for sponge layer code in external_forcing
4552     o modified test cost functions
4553     o storing in gad_advection (plus removal of write(0,*)!
4554     o missing headers TR1.h added in convective_adjustment routines
4555     o errorMessageUnit set non-equal zero in eeboot
4556     (conflict on some platforms, e.g. IBM SP3)
4557     o modified carbon verif.
4558    
4559 jmc 1.1203 checkpoint44h_pre (2002/03/14)
4560 jmc 1.68 o vertical grid option: allow to put the Interface at the middle between
4561     2 cell-centers ; replace delZ in pkg/kpp by drF.
4562 jmc 1.67 o GM Advective form: Tracers are advected using the residual transport (=
4563     Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
4564 jmc 1.66
4565 jmc 1.1203 checkpoint44g_post (2002/03/05)
4566 jmc 1.66 o fix surface correction term in multiDimAdvection (affects plume_on_slope
4567     results) ; ifdef missing in thermodynamics.F
4568 adcroft 1.65
4569     checkpoint44f_pre,checkpoint44f_post
4570     o added PTRACERS package
4571     This allows an arbitrary number of passive tracers to be integrated
4572     forward simultaneously with the dynamicaly model.
4573     + Implemented so far:
4574     - basic forward algorithm (time-stepping, advection, diffusion, convection)
4575     - I/O and checkpointing
4576     - GM/Redi *but* using the GM/Redi coefficient of Salt
4577     + Not implemented so far:
4578     - KPP
4579     - OBCS
4580     + No specific example supplied (yet) but global_ocean.90x40x15 has the
4581     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
4582     line in data.pkg.
4583     + This package is disabled by default since it increases storage.
4584    
4585 jmc 1.60
4586 adcroft 1.64 o testscript: added -cleanup option
4587 jmc 1.63 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
4588     b) enable to filter 2D fields.
4589 adcroft 1.62
4590     checkpoint44e_pre,post
4591     o re-wrote convective adjustment to use pre-calculated weights
4592     Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
4593     Adds: model/src/convective_weights.F, convectively_mixtracer.F
4594     Original calls to convect() still in place.
4595 heimbach 1.61
4596     chkpt44d_pre,post
4597     o added missing EXCLUDE_MONITOR flags
4598     o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
4599     (incompatible typ in MIN/MAX expressions caused problems
4600     on IBM SP3)
4601     o in genmake added variable MAKEDEPEND
4602     plus resetting for case SunOS
4603     o added timer_stats.c routine for IBM SP3
4604     o removed variables in dynamics
4605     !!! I forgot to create tag chkpt44d_pre !!!
4606     !!! But chkpt44d_pre = chkpt44c_post !!!
4607 jmc 1.63
4608     o real fresh water flux implemented with non-linear free-surface.
4609 heimbach 1.58
4610 jmc 1.59 chkpt44c_pre,post
4611     o few fix (mask in shap_s2, EmPmR in external_field_load,
4612     USE_NATURAL_BCS in solve_for_P);
4613     o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
4614    
4615 heimbach 1.58 checkpoint44b_pre/_post
4616     o merge of relevant stuff from the ecco-branch:
4617     - genmake: removed $S64 overwrite for case SunOS
4618     - pkg/exf: update and corrections for field swapping and obcs
4619     - pkg/ecco: parameter lists for the_model_main, the_main_loop
4620     harmonized between ECCO and MITgcm
4621     - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
4622     updated checkpointing_lev... lists for obcs
4623     - model/src: minor changes in forward_step, plot_field
4624     added directive for divided adjoint in the_main_loop
4625     - pkg/mdsio: added mdsio_gl_slice
4626 jmc 1.57
4627     o check parameters & config (chkpt44a_pre,post)
4628 jmc 1.56 o OBC and NonLin_FrSurf.
4629    
4630 jmc 1.1203 checkpoint44 (2002/01/18)
4631 jmc 1.54 o fix bug in mom_vi_del2uv
4632 jmc 1.56 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
4633     o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
4634     o update AIM experiments (NCEP input files)
4635     o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
4636 heimbach 1.55 o added some stuff for AD
4637 adcroft 1.53
4638 jmc 1.1203 checkpoint43 (2001/09/28)
4639 adcroft 1.53 o added two new advection tests
4640     o added global 4x4 degree ocean test
4641     o added test of H&S94 with free surface on cube
4642     o some final mods for gradient check, adjoint,...
4643 heimbach 1.52
4644 jmc 1.1203 checkpoint42 (2001/09/27)
4645 heimbach 1.52 Fixed AD-related problems:
4646     o Store directives up-to-date with re-arranged Adams-Bashforth
4647     (mainly thermodynamics.F)
4648     o New store directives for multi-dim. advection schemes
4649     * new CPP flag ALLOW_MULTI_DIM_ADVECTION
4650     * new common block and key passkey
4651     (mainly gad_advection.F)
4652     o Modified store directives for split of dynamics/thermodynamics
4653     for the case ALLOW_KPP
4654     o Cleaned argument list for timestep_tracer.F
4655 adcroft 1.51
4656 jmc 1.1203 checkpoint41 (2001/09/27)
4657 adcroft 1.51 o re-formatted/added comments in prologues of key subroutines
4658     to work with protex
4659 heimbach 1.47
4660 jmc 1.1203 checkpoint40 (2001/09/27)
4661 adcroft 1.50 o moved calc_gs, calc_gt and calc_tr1 back to model/src
4662     o added FLT (floats) package from Arne along with demo. experiment
4663     o re-arranged Adams-Bashforth scheme for tracers to allow easier
4664     implementation of forward-in-time forcing terms
4665     o more mods for non-linear free-surface including new variable
4666     o modified multi-dim method to work on cube
4667     o bug fix in KPP (from DM)
4668    
4669 jmc 1.1203 checkpoint40pre9 (2001/09/27)
4670 adcroft 1.49 o added DST advection schemes
4671     o fix MPI bug on SGI's
4672     o modifications for non-linear free-surface
4673     o fixed conditionals for fixed flow/passive tracer only mode
4674     o added tension/strain form of stress tensor
4675     o changes to commenting of arguments for TAF/TAMC
4676     o added/updated many matlab scripts
4677 adcroft 1.50 o added multi-dimensional advection method for tracers
4678 adcroft 1.49
4679 jmc 1.1203 checkpoint40pre8 (2001/09/05)
4680 heimbach 1.47 o new package rw/
4681     Added method for dumping intermediate local arrays:
4682     mdsio_writetile - same as mdsio_writefield except works from inside
4683     bi,bj loop
4684     mdsio_writelocal - same as mdsio_writetile except works for local
4685     arrays
4686     write_local_r? - higher-level wrapper for mdsio_writelocal
4687     Controlled by diagFreq. Defaults to zero (ie. no dumps)
4688     Example given at end of mom_vecinv.F that dumps some local arrays.
4689     o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
4690     control flux-form versus vector invariant code.
4691     Switch is runtime flag vectorInvariantMomentum (defaults to false)
4692     or genmake -DISABLE ...
4693     o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
4694     (additional storing is now needed for case vecinv;
4695     currently nothing implemented to switch this storing off
4696     in case fluxform is used since no CPP flag available).
4697 heimbach 1.46
4698 jmc 1.1203 checkpoint40pre7 (2001/08/14)
4699 heimbach 1.46 o bug fix in dynamics.F
4700     calc_viscosity called before k=1,Nr loop.
4701     o added some #ifdef's ALLOW_PASSIVE_TRACER
4702     o cleaned initialisations in ctrl_map_ini
4703     related to TAF
4704 heimbach 1.45
4705 jmc 1.1203 checkpoint40pre6 (2001/08/13)
4706 heimbach 1.45 o split dynamics into thermodynamics & dynamics
4707     o corresponding split of calc_diffusivity into
4708     calc_diffusivity, calc_viscosity
4709     (kpp_calc_diff, kpp_calc_visc).
4710     o Added diffkr, kapgm to control variables
4711     o bug fix in gmredi_slope_limit for ldd97
4712 adcroft 1.44
4713 jmc 1.1203 checkpoint40pre5 (2001/07/31)
4714 adcroft 1.44 o proper initialization of Adams-Bashforth time stepping
4715     + uses forward step for very first step of model (iter=0)
4716     o re-generated *all* output since almost all output is modified by this
4717     change (sorry but we've been putting this one off for about 2 years)
4718     + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
4719     *not* regenerated since they are already out of date and I don't
4720     want to create the impression that they are suddenly working.
4721     o removed KAP stuff for DEC's
4722     o modified/added many .cvsignore files in */code and */input
4723     o added new expt "solid-body.cs-32x32x1"
4724     + this uses an alternative form of ini_curvilinear_grid.F which
4725     is not necessarily any better than the current one...
4726 heimbach 1.43
4727 jmc 1.1203 checkpoint40pre4 (2001/07/30)
4728 heimbach 1.43 o added re-initialisations of utrans,vtrans,rtrans in
4729     calc_common_factors which are crucial for TAF.
4730     o extended iMin,jMin range for calc_common_factors,
4731     calc_diffusivity
4732     o added option ALLOW_PASSIVE_TRACER
4733     o a few minor updates and fixes
4734    
4735 jmc 1.1203 checkpoint40pre3 (2001/07/13)
4736 heimbach 1.42 o created calc_gtr1.F for gad package
4737     o split the_main_loop and re-introduced forward_step
4738     o some recomputations of nIter0 for TAMC
4739    
4740 jmc 1.1203 checkpoint40pre2 (2001/07/13)
4741 heimbach 1.41 o Updated to latest branch of AJA, JMC
4742     o Added gradient check package
4743     o Added routines for passive tracer handling
4744     o Added carbon sequestration sensitivity experiment
4745    
4746 jmc 1.1203 checkpoint39 (2001/05/14)
4747 heimbach 1.39 o Modifications and fixes to support TAMC
4748     (mainly missing or wrong directives)
4749     o Corrected common blocks when fooling TAMC to produce adjoint I/O
4750     in addummy_in_stepping
4751     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
4752     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
4753     o Included following packages:
4754     cal: calendar
4755     exf: external forcing
4756     ecco: essential routines to control use of cal, exf
4757     (NB: this is not the full ECCO environment)
4758 heimbach 1.40 o disabled some packages by default in genmake
4759 heimbach 1.39
4760 jmc 1.1203 checkpoint38 (2001/04/10)
4761 heimbach 1.38 o see notes_c37_adj.txt
4762     o corrected wrong layer index in external_forcing_t
4763     o replaced the_main_loop/forward_step by the_main_loop
4764     o removed forceoutput from write_state
4765     (replaced criteria for initial/final state)
4766     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
4767 jmc 1.36
4768 jmc 1.1203 checkpoint37 (2001/03/13)
4769 jmc 1.37 o mdsio.F routine split and packaged in pkg/mdsio
4770     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
4771     used unless genmake -disable=mdsio)
4772     o allow a more precise surface-geopotential gradient for the atmosphere
4773     taking into account the change in space of Alpha (=1/rho) at the surface.
4774     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
4775     (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
4776     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
4777     Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
4778     [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
4779     o Time-Average diagnostics defined as a pseudo package "timeave".
4780     o pickup files : old pickup (before c35) did not work with new code (c35
4781     and after) unless activating 2 commented lines in initialise-varia.
4782     o Non-Hydrostatic pickup file Pb fixed.
4783     o bug with Rigid-lid version (since c35) fixed.
4784    
4785 jmc 1.1203 checkpoint36 (2001/02/20)
4786 jmc 1.37 o implement Crank-Nickelson barotropic time-stepping
4787 jmc 1.36 o recover Time-Average diagnostics
4788     o fix Pb in checkpoint (PR#19)
4789     o AIM become a standard package ; clean unused CPP_kees
4790 jmc 1.35
4791 jmc 1.1203 checkpoint35 (2001/02/08)
4792 jmc 1.35 o subtantial rewrite of dynamics.f
4793     o allows staggered time-stepping
4794     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
4795     o added bottom drag (linear + quadratic)
4796 heimbach 1.33
4797 jmc 1.1203 checkpoint34 (2001/01/30)
4798 heimbach 1.33 o Modified exchange routines for correct reverse simulation.
4799     o Added verification output to comply with bug fix in impldiff.F
4800     as of c33 (exp2, natl_box).
4801     o Corrected store directives in dynamics.F
4802     o Corrected array boundaries in impldiff.F
4803     o Corrected array dimensions in gmredi.
4804     Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
4805 heimbach 1.34 o Added routine GLOBAL_SUM_INT to global_sum.F
4806 heimbach 1.33 o Added mdsio_gl.F for ECCO purposes.
4807 adcroft 1.32
4808 jmc 1.1203 checkpoint33 (2000/11/30)
4809 adcroft 1.32 o Fixed bug in lower BC in impldiff.F
4810     o Fixed confusion about units of forcing arrays in FFIELDS.h
4811     namely Fu,Fv,Qnet,Qsw,EmPmR:
4812     - Removed verification/natl_box/code/external_fields_scale.F
4813     (did not differ from that in model/src)
4814     - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
4815     (see FFIELDS.h for description)
4816     - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
4817     kpp_calc.F and kpp_transport_t.F
4818     - Removed model/src/external_fields_scale.F and calls to it
4819     - verification/natl_box uses flux data with "atmospheric" sign so
4820     a special version of external_fields_load.F is used to
4821     change the data as it's read in. This way, the arrays
4822     have the right units and signs at all times tha a user could
4823     possibly use them.
4824     o Corrected genmake to delete a temporary file during configuration
4825 heimbach 1.31
4826 jmc 1.1203 checkpoint32 (2000/11/13)
4827 heimbach 1.31 o Scaling of forcing fields moved from external_forcing.F to
4828     external_fields_scale.F, called directly after loading fields.
4829     o Surface relaxation terms added to surface tendency fields in
4830     extra subroutine.
4831     o impldiff.F changed to avoid storing by TAMC of huge intermediate
4832     fields.
4833     o Changes in GMRedi to comply with packaging structure.
4834     o Modifications and bug fixes in KPP package.
4835     o Verification experiment for KPP added (verification/nat_box/)
4836 heimbach 1.30
4837 jmc 1.1203 checkpoint31 (2000/09/11)
4838 heimbach 1.30 o Packages interface brought in line with defined standard
4839     -> new routines packages_...F
4840     -> changes in initialise_fixed.F, initialise_varia.F
4841     -> enables initialisation interface for ECCO package
4842     o Rescaling of external forcing fields immediately after read
4843     (removed from external_forcing.F)
4844     -> new: surface_fields_scale.F
4845     -> affects ini_foorcing.F, external_fields_load.F
4846     o Computation of surface tendencies before tendency updates.
4847     -> new: external_forcing_surf.F
4848     o Change of variable names useGMRedi, useKPP, useECCO
4849     o Further changes in dynamics.F, impldiff.F for TAMC
4850     o Tested for experiments 0, 2, 4.
4851     - not yet tested for GMRedi.
4852     - not yet tested for KPP.
4853 adcroft 1.29
4854 jmc 1.1203 checkpoint30 (2000/07/13)
4855 adcroft 1.29 o Updates for OBCs
4856     o New experiment for test OBCs (internal_wave)
4857     o New output.txt in verification/exp4/results/
4858     o Updates for KPP: calculation of viscosity corrected, new variables
4859     kpp_dumpFreq and kpp_taveFreq
4860     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
4861     and entry for T90 in genmake
4862 adcroft 1.28
4863 jmc 1.1203 checkpoint29 (2000/06/21)
4864 adcroft 1.28 o packaged KPP and GM/Redi
4865 heimbach 1.27
4866 jmc 1.1203 checkpoint28 (2000/06/09)
4867 heimbach 1.27 o Corrected initialization of hFacMin for difference vertical coordinates
4868     o Modified calculation of partial cell thickness to more robust algorithm
4869     o config_summary.F: replaced write_1D_... by write_0D_...
4870     read_write.F: added subroutines write_0D_...
4871     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
4872     included some initialisations required for TAMC.
4873     o routine calc_isoslopes: modified sqrt computation to make it
4874     differentiable for zero argument.
4875     o routines dynamics, impldiff:
4876     included store directives and tape key computations required for TAMC.
4877     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
4878 adcroft 1.26
4879 jmc 1.1203 checkpoint27 (2000/04/10)
4880 adcroft 1.26 o fixed calc_isoslopes() to so that cancellation of terms in tensor
4881     formulation works properly with variable resolution.
4882     o restructured the calling tree between the_model_main() and dynamics()
4883     o split initialise() into initialise_fixed() and initialise_varia()
4884     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
4885     in new routine ini_psurf()
4886 adcroft 1.25
4887 jmc 1.1203 checkpoint26 (2000/04/05)
4888 adcroft 1.25 o moved some #ifdef in optional routines to encompass everything
4889     except the argument declarations. This was using up some memory.
4890     o fixed macros like _ADT to work with both versions of Linux cpp
4891     o cleaned up some unused and uninitialized variables
4892     (helps when debugging with strict compile options)
4893     o split up CPP_EEOPTIONS.h into options and macros
4894     (macros are now in eesupp/inc/CPP_EEMACROS.h)
4895     o patch for 2 processor JAM mode
4896 adcroft 1.24
4897 jmc 1.1203 checkpoint25 (2000/03/15)
4898 adcroft 1.24 o updates for OBCs and NH
4899     o dramatically reduced memory usage
4900     o added "JAM" routines for use on Artic network
4901     o parameterization of convection by implicit vertical diffusion
4902     o added a diagnostic of convective index
4903     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
4904     (this is was partly for OBCs and NH but also in anticipation of
4905     an explicit free-surface option)
4906     o initial state input files for U and V
4907 adcroft 1.23
4908 jmc 1.1203 checkpoint24 (1999/08/02)
4909 adcroft 1.23 o Removed some spurious "REAL"s
4910     o Updated KPP to latest version from JPL
4911     o Added a COS(latitude) in horizontal viscosity
4912 adcroft 1.22
4913 jmc 1.1203 checkpoint23 (1999/05/26)
4914 adcroft 1.22 o Added del^4 diffusion for salt and temperature
4915     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
4916 adcroft 1.21
4917 jmc 1.1203 checkpoint22 (1999/05/18)
4918 adcroft 1.21 o Made many small changes: implicit none, format(i5), etc...
4919     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
4920 adcroft 1.20
4921 jmc 1.1203 checkpoint21 (1999/05/18)
4922 adcroft 1.20 o Introduced new I/O package that supports direct-access records (mdsio.F)
4923     o Split-up mid-level I/O routines
4924     o Updated input data for experiments 0,1,2,4 and 5
4925     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
4926 adcroft 1.18
4927 jmc 1.1203 checkpoint20 (1999/03/22)
4928 adcroft 1.19 o Tidied up open-boundaries some more
4929     o Added non-hydrostatic code
4930     o Fixed some input data
4931     o Modified MPI start-up to work in "coupled" context.
4932    
4933 jmc 1.1203 checkpoint19 (1998/12/15)
4934 adcroft 1.18 o Tidied up directory structure for verification experiments.
4935     o Added new code for open boundaries.
4936     o Corrected advective terms near boundaries.
4937     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
4938     o Implemented free-slip/no-slip BCs and del^4 dissipation.
4939 adcroft 1.19 o Split default parameters out of ini_parms.F into set_defaults.F.
4940 cnh 1.17
4941 jmc 1.1203 checkpoint18 (1998/11/30)
4942 cnh 1.17 o Further changes for optional code generation with
4943     CPP - ugh!
4944 cnh 1.16
4945 jmc 1.1203 checkpoint17 (1998/11/03)
4946 cnh 1.16 o Beginning to incorporating modularity
4947     for supporting atmos. and ocean configs.
4948     o Small changes for TAMC complinace
4949     o New ultra simple test case. Barotropic box
4950     configuration "exp0".
4951 cnh 1.15
4952 jmc 1.1203 checkpoint16 (1998/10/28)
4953 cnh 1.15 o Minor changes to exchange routines to support
4954     accumulation in reverse mode. Adjoint of an
4955     assignment is an addition.
4956     o Changes to support compilation by TAMC (LR(1)
4957     syntax) and by g77 under Linux ( 72 character
4958     limit ).
4959 cnh 1.14
4960 jmc 1.1203 checkpoint15 (1998/09/29)
4961 cnh 1.14 Rewrote exchange routines to allow
4962     o General tile <-> tile connectivity.
4963     o TAMC reverse mode flag ( is this really needed? )
4964     o Variable width overlap and exchange region widths.
4965     o Hooks for sharing data via DMA, Arctic, Memory Channel,
4966     shmput/shmget, VIA, SYSV shmem and every other cool
4967     communication method.
4968 cnh 1.13
4969 jmc 1.1203 checkpoint14 (1998/09/09)
4970 cnh 1.13 Consistent isomorphism chages made. These allow dynamical core
4971     to support both pressure and meters as a vertical coordinate.
4972 cnh 1.12
4973 jmc 1.1203 checkpoint13 (1998/07/17)
4974 cnh 1.12 Release which corrects global_max problem and a couple
4975     of KGM time-averaging diagnostic errors. Also contains
4976     a double-gyre experiment setup as well as the baseline
4977     4 degree global template. The double gyre template is
4978     organised to allow it to be applied automatically to
4979     the baseline configuration.
4980 adcroft 1.11
4981     branch-point-rdot
4982     A few tidy-ups have been made bt the real point of this
4983     check-point (excuse the pun) is to allow a branch to be
4984     made for the purposes of adding the rDot alterations.
4985     I don't want to commit the rDot to the main-trunk until
4986     we've actually tested it...
4987 cnh 1.10
4988 jmc 1.1203 checkpoint12 (1998/07/08)
4989 cnh 1.10 Tidy up and added generic genmake script (formerly
4990     configure script).
4991     Released to testers.
4992 adcroft 1.9
4993 jmc 1.1203 checkpoint11 (1998/07/02)
4994 adcroft 1.9 Re-arranged initialise() and introduced ini_vertical_grid()
4995     and ini_masks_etc().
4996 adcroft 1.8
4997 jmc 1.1203 checkpoint10 (1998/07/01)
4998 adcroft 1.8 Introduced the configure script.
4999     Separated out the diags package.
5000     Added template for writing time-averages of tile/intermediate quantities.
5001     Updated SIZE.h in exp2 and made the data big-endian.
5002 adcroft 1.7
5003 jmc 1.1203 checkpoint9 (1998/06/22)
5004 adcroft 1.7 MPI fix. Filename changes (meta/data). salbin*y stuff.
5005     General tidy-up.
5006     SST.bin SSS.bin added to verification/exp2
5007 adcroft 1.6
5008 jmc 1.1203 checkpoint8 (1998/06/22)
5009 adcroft 1.6 Inludes time-dependant forcing and time-averaging.
5010     Works at 4x4 and 2.8125x2.8125 global
5011    
5012     checkpoint7-4degree-ref
5013     Branch from checkpoint7. Released for application to
5014     global modeling and general modeling - process studies, regional
5015     model etc..
5016     Configured for verification/exp2 - 4 degree global, two process.
5017 cnh 1.5
5018 jmc 1.1203 checkpoint7 (1998/06/15)
5019 cnh 1.5 Created by cnh
5020     Simple 4 degree global simulation
5021     configuration.
5022     Includes climatological wind,
5023     hydrography, bathymetry etc
5024     Does not include Heat Flux and E-P
5025 cnh 1.4
5026 jmc 1.1203 checkpoint6 (1998/06/08)
5027 cnh 1.4 Created by cnh
5028     merged checkpoint5 with CD and
5029     spherical polar code.
5030     Still some problems with GM Redi
5031     abd full topography.
5032 cnh 1.3
5033 jmc 1.1203 checkpoint5 (1998/06/08)
5034 cnh 1.3 Created by AJA
5035     contains updates to GM Redi
5036     and reordered timestepping loop
5037     for Implicit Diffusion.
5038 cnh 1.2
5039 jmc 1.1203 checkpoint4 (1998/05/30)
5040 cnh 1.2 Created by cnh
5041     Contains memory saving macros ( _rdxc etc..) for when
5042     grid variations are limited.
5043     Contains polynomial coeffs for EOS and knudsen program
5044     for generation.
5045    
5046 jmc 1.1203 checkpoint3 (1998/05/26)
5047 cnh 1.1 Created by cnh
5048     Added extra flags for runtime options
5049     Added this file
5050     Added implicit free-surface
5051     Added pre-conditioner
5052     Put compare01 into repository ( compare01/... )
5053     Put data and eedata into repository ( verification/exp1 )
5054    
5055     checkpoint2
5056     Created by AJA
5057     Added GM/Redi
5058    
5059     checkpoint1
5060     Created by AJA
5061     Restructured kloop in dynamics.F
5062     Added non-linear EOS
5063    
5064 cnh 1.2 baseline
5065     Original checked in code
5066 cnh 1.1

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