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Revision 1.1138 - (hide annotations) (download)
Tue Jun 30 16:38:02 2009 UTC (14 years, 10 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint61s
Changes since 1.1137: +2 -1 lines
checkpoint61s

1 jmc 1.1138 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1137 2009/06/30 00:02:32 jmc Exp $
2 jmc 1.475 $Name: $
3 cnh 1.1
4     Notes on tags used in MITgcmUV
5     ==============================
6 mlosch 1.755
7 jmc 1.1138 checkpoint61s
8 jmc 1.1137 o pkg/exch2 (exch2_rxN_cube*):
9     remove last BARRIER (no need to synchronise after getting data from shared
10     buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
11 jmc 1.1136 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
12     and generate new output (for the 2 tests) using default rotationPeriod.
13 jmc 1.1135 o pkg/exch2:
14     - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
15     (was already the case with AUTODIFF_EXCH2 defined)
16     - add bj in exch2 arrays and S/R.
17 jmc 1.1136 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
18     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
19 jahn 1.1134 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
20     - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
21     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
22     - verification experiment natl_box.longstep
23 jmc 1.1133 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
24     allow different versions of ifort (8 or 9) and different versions
25     of mpi (mpich or mpich2) to be used with the same optfile.
26     requires to load a netcdf module and set MPI_INC_DIR (see comments inside
27     optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
28 jmc 1.1135 o pkg/seaice:
29     fix previous modif (3-level field removed) for old-pickup reading
30 jmc 1.1133
31 jmc 1.1132 checkpoint61r
32 mlosch 1.1129 o pkg/seaice:
33 mlosch 1.1130 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
34     1. introduce fields for time step (N-1)
35     2. do not use levels 2 and 3 anymore (but keep them)
36     3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
37     includes changes to pkg/thsice/thsice_get_velocity.F,
38     model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
39     pkg/obcs/obcs_apply_uvice.F.
40     - completely remove code for leap-frog time stepping for second order
41 mlosch 1.1129 advection
42 heimbach 1.1131 - adjusted adjoint accordingly;
43     gradient checks have improved by an order of magnitude!
44 mlosch 1.1130
45 mlosch 1.1128 checkpoint61q
46     o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
47     - the boundary conditions along open boundaries are unclear, because the
48     associated masks are set to zero and are thus treated as closed when
49     applying the slip-boundary conditions.
50     - move initialisation of grid variables from seaice_init_varia to _fixed
51 dimitri 1.1127 o adding doc/diags_changes.txt
52 jmc 1.1126 o model/src:
53     do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
54     to avoid "_diags" naming if no relation to pkg/diagnostics.
55     ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
56     file and only call PLOT_FIELD_XYZ if debugMode=T.
57     remove few PLOT_FIELD_XY calls outside initialisation.
58     remove few unnecessary BARRIER.
59 dimitri 1.1125 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
60     of salt_plume package in Southern Ocean
61 jmc 1.1124 o pkg/thsice:
62     - fix hOceMxL in overlap (needed for sea-ice advection);
63     update output of experiment global_ocean.cs32x15.icedyn.
64 mlosch 1.1123 o pkg/seaice:
65     - make the (placeholder-)tracer IceAge a little more meaningful
66 mlosch 1.1122 by avoiding ridging of age due to convergent ice flow
67 dimitri 1.1127 - add diagnostics for surface temperature, atmospheric and oceanic
68     heat flux, and atmospheric and oceanic ice growth
69 mlosch 1.1122
70 jmc 1.1121 checkpoint61p
71 jmc 1.1120 o eesupp (global_max & global_sum):
72     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
73     - remove starting & endding barrier (no longer needed)
74 jmc 1.1119 o pkg/mdsio, writelocal:
75     works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
76     (remove the STOP): uses shared buffer IO to store data from all threads
77     and then let master-thread write nThreads tiles.
78 jmc 1.1118 o pkg/mdsio (read/write field):
79     - tiled IO done in 1 piece (all levels at a time);
80 jmc 1.1119 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
81 jmc 1.1118 - multi-threaded: allow to read/write local (non-shared) array
82     (was already working with singleCpuIO ; now works also without);
83     => no longer needs barrier call after reading a file (added inside
84 jmc 1.1119 mds_read/write field).
85 jmc 1.1118 - move barrier calls outside gather/scatter_2d to mds_read/write_field
86 mlosch 1.1115 o pkg/obcs/exf
87 mlosch 1.1116 - exf_getffieldrec.F: add a few ". _d 0" and
88     add code to catch the case fldperiod = 0.
89 mlosch 1.1115 - obcs_precribe_read.F: change if statements so that they match
90     the variable type (_RL)
91     - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
92     exf_iprec) as part of namelist EXF_NML_01
93 jmc 1.1114 o pkg/mdsio:
94     - read/write tiled (local) files: read/write 1-level tile chunk at a time
95     (instead of segment of length sNx); expected to speed up tiled IO.
96     o pkg/exch2:
97 jmc 1.1113 - take buffer copy from/to array out of S/R exch2_send/recv into new
98     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
99     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
100     - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
101 jmc 1.1114 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
102 jmc 1.1113 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
103     including Topology header file (and common blocks).
104     - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
105     remove 2nd exch call in exch2_s3d_rx (no longer needed).
106     - document S/R arg. list (+ update some comments)
107 dimitri 1.1117 o pkg/seaice:
108     - added SEAICE_CLIM_AIR code, which permits modulation of surface air
109     temperature and humidity over sea ice based on climatological values.
110 mlosch 1.1111 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
111     of LSR (this change is expected to change the results slightly because now
112     it uses slightly difference moduli from the second last LSR solution, but
113     that is more consistent with the stress computations; this part of the code
114     is not tested in the verification experiments)
115 mlosch 1.1110 - fix diagnostics for flux of ice in case of B-grid
116     - turn strain rates eij and press into global fields within global
117     common block in SEAICE.h for more straighforward diagnostics
118     - fix diagnostics for principal stress components, press, zeta, eta
119     to give something meaning full
120 jmc 1.1109 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
121     new output (all 4 tests) using default rotationPeriod.
122 dfer 1.1112 o pkg KPP:
123     - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
124     - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
125     and normal grid from 1 to Nr)
126 dfer 1.1108 o Fix computations of L4rdt in mom_calc_visc.F
127 jmc 1.1107 o eesupp:
128     new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
129     should be called before a "stop" if we know that all process are going
130     to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
131    
132 jmc 1.1106 checkpoint61o
133     o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
134     o model/src/ini_curvilinear_grid.F:
135 mlosch 1.1104 compute angleSin/CosC when they are not read from a file
136 jmc 1.1106 o pkg/seaice:
137 mlosch 1.1104 add pseudo time stepping for LSOR
138 jmc 1.1103 o pkg/exch2:
139     temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
140 dimitri 1.1102 o pkg/seaice:
141 dimitri 1.1105 Adding separate sea ice albedo, drag coefficients, and HO in Southern
142     Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
143 jmc 1.1101 o SingleCpuIO:
144     fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
145     o pkg/seaice:
146 jmc 1.1100 put exchanged variable in (local) common block for MPI+Multi-Threads
147     to work (necessary with exch1, and for now with exch2 too).
148 jmc 1.1099 o verification: to get more experiments tested with mpi, mth and mpi+mth,
149     change tiling of:
150     aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
151     hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
152     update output of exp:
153     exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
154     tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
155     + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
156     (note: output.txt generated on faulks using only 1 tile)
157 jmc 1.1098 o eesupp & mdsio (SingleCpuIO):
158     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
159     parameter "W2_useE2ioLayOut" (read from file "data.exch2").
160     Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
161     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
162     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
163     gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
164 jmc 1.1097 o pkg/exch2:
165     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
166     read parameter file "data.exch2" if it exists; otherwise try default regular
167     cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
168     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
169     with new code (not to be used, just as a backup solution).
170 jmc 1.1098 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
171     in utils/exch2/input.
172 jmc 1.1097
173 jmc 1.1096 checkpoint61n
174 jmc 1.1095 o eesupp & mdsio (SingleCpuIO):
175     - move mapping to global io-buffer inside gather_2d/scater_2d: this save
176     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
177     receive real*4 array (instead of real*8) to read/write 32.bit files.
178     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
179     and remove new mapping S/R)
180 jmc 1.1094 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
181     - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
182     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
183     when using exch2. Add S/R to map global io-buffer to global model array.
184     - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
185    
186 jmc 1.1093 checkpoint61m
187 jmc 1.1094 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
188     and add 3 other S/R for other types (R4,R8,RS).
189 jmc 1.1092 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
190     o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
191     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
192     - reduce number of macro definitions (keep only those which are used);
193     can always call directly the corrresponding S/R if needed.
194 jmc 1.1094 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
195 jmc 1.1092 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
196     Fixed wrong type of arg in:
197 jmc 1.1094 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
198 jmc 1.1092 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
199     To fix: global_sum of var in common block is wrong (multi-threaded) in:
200     dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
201     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
202 jmc 1.1094 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
203     "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
204 jmc 1.1091 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
205     o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
206     edges are closed (zero depth); might happen with "blank tiles";
207 jmc 1.1094 for now, disabled if using OBCS.
208 jmc 1.1091 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
209 jmc 1.1090 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
210 jmc 1.1091 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
211 jmc 1.1089 to reduce length of 1.D array print in STDOUT.
212 jmc 1.1088 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
213     + use 48 tiles (16x8): this will allow to test "blank tiles".
214     o start to test MPI + multi-threaded (change testreport to skip tests
215     where number of tiles do not match).
216     o genmake2: add option "-omp" to turn on Open-MP ;
217     passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
218 jmc 1.1086 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
219     and keep the original tile numbering. Note: compatible with old
220     W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
221    
222 jmc 1.1085 checkpoint61l
223     o Overlaps had been forgotten in calculating ijk keys : fixed
224     o fix cyrus makedepend for gcc 4.4
225 jmc 1.1084 o experiment fizhi-cs-aqualev20:
226     switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
227 jmc 1.1088 and generate new output. Note: new output is much closer to the old
228     one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
229 jmc 1.1084 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
230     o pkg/fizhi:
231     - change to avoid indices going deliberately over array-bounds
232     - remove unnecessary MPI stuff
233     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
234     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
235     does not go over array-bounds and therefore returns reliable output.
236     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
237     this S/R has 4 output arguments, which are used inside "get_alarm";
238     when it is called with the same variable "ndum" in place of several
239     output arguments, this produces weird side effect inside "get_alarm"
240     (e.g., datein=dates(n) is overwritten by timein=times(n) since both
241     datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
242     address) and produces error.
243 jmc 1.1090 o tools/gemake2: (March 27-29 2009)
244     with option "-mpi": link *_mpi files from "MODS" dir (this is what
245     testreport does).
246 jmc 1.1083 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
247 jmc 1.1084 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
248 jmc 1.1083 update lab_sea.lsr & lab_sea.salt_plume results
249 mlosch 1.1079 o pkg/seaice:
250     Major overhaul of the LSOR solver: change discretization from original
251     finite differences to finite volume. The old routine is still in the
252     file seaice_lsr.F and can be turned on with the CPP-flag
253     SEAICE_OLD_AND_BAD_DISCRETIZATION
254     Along with this change, the discretization of the strain rates is changed.
255     The same flag turns on the old discretization in seaice_calc_strainrates.F
256     All verification experiments with seaice are affected (except for
257     seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
258     results by setting the above flag.
259     Further changes involve changes in defaults:
260     - ALLOW_FLOODING is defined and turned on by default
261 heimbach 1.1087 - SEAICEadvSnow = .true. is now the default
262     - SEAICEadvSalt = .true. is now the default
263     - SEAICEadvAge = .true. is now the default
264 mlosch 1.1081 - SEAICE_clipVelocities = .false. is now the default
265     (as per J. Zhang's recommendation)
266 mlosch 1.1079 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
267     is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
268     - seaice_growth: replace computation of UG by a simple copy from wspeed
269    
270 mlosch 1.1078 checkpoint61k
271     o pkg/seaice: a few bug fixes mostly concerning the metric terms:
272     seaice_lsr: fixed a few metric terms,
273     affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
274     add more debugging diagnostics
275     seaice_evp: removed superfluous many metric terms of FV discretization
276     of stress divergence
277     affects lab_sea, lab_sea.hb87
278     seaice_ocean_stress: removed superfluous many metric terms of FV discretization
279     of stress divergence for non-evp solver
280     (this part is not tested anywhere)
281     seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
282     they were effectively only half slip
283     affects lab_sea.hb87
284 jmc 1.1082 updated all relevant verification experiments (except lab_sea//output_adm.txt
285     which was left over, but fails at level 7 & 6)
286 mlosch 1.1078
287 heimbach 1.1077 checkpoint61j
288 mlosch 1.1076 o pkg/seaice: turn a few hard wired parameters into run time parameters
289 mlosch 1.1075 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
290     time in seconds as promised by the usints in seaice_monitor and exf_monitor
291 mlosch 1.1074 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
292     that are not cubed-sphere grids
293 mlosch 1.1073 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
294 jmc 1.1072 o pkg/ctrl:
295     fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
296 jmc 1.1071 o non-hydrostatic (calc_gw.F):
297     fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
298     update output of exp. global_ocean.cs32x15.viscA4
299     o remove backward compatibility for thetaMin,phiMin
300 jmc 1.1070 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
301 mlosch 1.1069 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
302     interpolated wind field not only for curvilineargrid=.true., but also
303     for a rotated grid (rotateGrid=.true.)
304 mlosch 1.1068 o pkg/exf: add capability to bypass interpolation for runoff
305     by setting yet another CPP-flag
306 jmc 1.1070 o eesupp/src, B-grid exchange:
307     add simple (6 tiles, non MPI) CS exch + standard interface S/R.
308 heimbach 1.1067 o autodiff
309     new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
310     allows to switch to single-prec common blocks;
311     corresponding switch occurs in tamc.h, integer isbyte
312     TAF store directivs "byte" and "kind" seem equivalent;
313     Most tamc.h have been updated correspondingly.
314    
315 heimbach 1.1066 checkpoint61i
316     o autodiff:
317     fix autodiff_sore/_restore indices for obcs
318     (spotted by I. Hoteit, M. Mazloff)
319 heimbach 1.1065 o pkg/autodiff, pkg/ctrl:
320     Add flag to reduce all tapelev I/O to single-prec.
321     In data.ctrl set
322     doSinglePrecTapelev = .TRUE.
323 jmc 1.1070 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
324     check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
325 mlosch 1.1062 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
326     real fresh water flux (not yet)
327 jmc 1.1060 o pkg/mdsio & rw:
328     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
329     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
330 jmc 1.1058 o pkg/flt:
331     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
332     init_fixed & ini_varia.
333 jmc 1.1059 - clean-up & simplify linear interpolation S/R:
334     move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
335     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
336 jmc 1.1060 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
337 jmc 1.1061 - add vert. coordinate & horiz. indices to output files.
338     - change vertical position in initial condition, from index to depth [m].
339 jmc 1.1063 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
340     (easier to get to a curvilinear grid) ; delX,delY no longer used.
341 dfer 1.1057 o pkg/ggl90: a few modifications:
342     - fix bottom boundary condition, and interpolation of KappaE
343     near top and bottom
344     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
345     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
346     - add a few options for mixing-length upper limit (--> mxlMaxFlag)
347 jmc 1.1056 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
348     (maintain temporary backward compatibility, until next checkpoint)
349    
350 jmc 1.1055 checkpoint61h
351 jmc 1.1054 o pkg/diagnostics with "periodic averaging diagnostics":
352     fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
353 jmc 1.1053 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
354 mlosch 1.1052 o pkg/obcs: fix loop ranges for balancing code
355 jmc 1.1051 o pkg/flt:
356     - improve criteria for finding which tile owns a float.
357     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
358 dfer 1.1050 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
359     aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
360     with ocean biogeo)
361 jmc 1.1049 o pkg/flt:
362     - do some cleaning and fix the restart ;
363     - add output.txt in flt_example/results to get this pkg tested.
364     o genmake2: add an EXTENDED_SRC option and flag.
365     for now, cannot be turned on on command line (only through genmake_local)
366 jmc 1.1048 o pkg/mdsio: read/write vector:
367     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
368 jmc 1.1049 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
369 jmc 1.1048 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
370     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
371     (drop to 4 digits matching for grad). But this test does not look very
372     reliable (was already failling on eddy, fc5, at 6.digits). Update output.
373    
374 jmc 1.1047 checkpoint61g
375 jmc 1.1046 o pkg/flt:
376     - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
377     + make OPTIONS file more standard.
378     - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
379     - fix _BYTESWAPIO CPP-Flag
380     - standard reading of file-parameter "data.flt"
381 jmc 1.1047 - fix argument list of S/R FLT_RESTART
382 jmc 1.1046 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
383 mlosch 1.1045 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
384 mlosch 1.1044 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
385     a still unfixed compiler/optimization bug
386    
387 jmc 1.1043 checkpoint61f
388 jmc 1.1042 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
389     update results of global_ocean.cs32x15.icedyn test.
390 jmc 1.1041 o move getcon.F from model/src to pkg/fizhi.
391 jmc 1.1040 o pkg/exf: add parameter for extrapolation of temp up to the surface
392     and option to prevent negative evap (in bulk_largeyeager04 only).
393 jmc 1.1039 o Prather Advection scheme: fix tracer conservation for divergent flow
394     (e.g., when using NonLin Free-Surface).
395 dfer 1.1038 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
396 jmc 1.1037 o gmredi (Visbeck-variable-K):
397     - add more parameters to Visbeck-variable-K.
398     - use a 5 points average for dSigmaR in Visbeck-K calculation
399     (more "homogenous": same stencil and same weights as in dSigmaH)
400     - update output of ideal_2D_oce experiment.
401 mlosch 1.1034 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
402     (#undef REAL4_IS_SLOW)
403     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
404     coordinate variable
405     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
406     (surface forcing fields), removes some of the functionality
407     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
408     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
409     probably not all: copy _RS surface flux fields to RL field before
410     calling DIAGNOSTICS_FILL
411 mlosch 1.1035 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
412     real*4 (CALL EXCH_*_RS) versions.
413 jmc 1.1036 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
414     (generate new output).
415 mlosch 1.1034
416 jmc 1.1033 checkpoint61e
417 jmc 1.1032 o gmredi (Visbeck-variable-K):
418     - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
419     - change computation of Visbeck-K where Slope > Smax :
420     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
421     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
422 jmc 1.1031 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
423     to be the same as with Z-coord. (i.e., m/s & no-units respectively).
424     o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
425 jmc 1.1030 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
426 jmc 1.1032 does not become too large (to avoid precision problems in implicit-diffusion
427 jmc 1.1030 solver); update ideal_2D_oce output.
428 dfer 1.1028 o pkg ggl90:
429     - in ggl90_cal.F: compute only one set of visc/diff, used to
430     step forward TKE/T/S/momentum
431     - default value of GGL90viscMax/GGL90diffMax larger and equal (to
432     have Prandlt =1)
433 jmc 1.1032 o gmredi (fm07):
434 jmc 1.1029 - add lower limit on Transition layer thickness + lower limit on 1/lambda
435 jmc 1.1027 - allow to set few more params from data.gmredi
436 dfer 1.1026 o pkg ggl90:
437     - add missing sqrt(2) factor in computation of mixing length
438     scale in ggl90_calc.F
439     (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
440    
441 heimbach 1.1025 checkpoint61d
442     o adjoint modifs
443     - adapt to new field rhoInSitu
444     - allow to revert from StoreDynVars2D, StoreDynVars3D
445     to individual fields
446     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
447 jmc 1.1024 o store 3-D (in-situ) density in commom block (DYNVARS.h)
448     - save 1 rho computation.
449     - no longer modify T & S inland when using down_slope pkg.
450 jmc 1.1023 o gad_som : allow to switch to SOM advection for T & S without corresponding
451     pickup files (using new S/R: MDS_CHECK4FILE).
452     o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
453     (for useSingleCpuIO to work in multi-threaded)
454 mlosch 1.1022 o pkg/shelfice:
455     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
456     with SHELFICEtopoFile in data.shelfice
457     - move code for reading ice shelf topography and modifying hFacC into separate
458     subroutines of the shelfice package
459     - separate initialisation of "fixed" and "variable" variables
460     - kTopC is not (yet) replaced by kSurfC, although this is possible
461 jmc 1.1023 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
462 jmc 1.1020 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
463     and rename:
464     ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
465     ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
466     o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
467    
468 jmc 1.1019 checkpoint61c
469 jmc 1.1018 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
470     to add mass source/sink of fluid in the interior (3-D generalisation
471     of oceanic real-fresh water flux).
472     o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
473 jmc 1.1017 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
474 jmc 1.1016 o new pkg: down_slope
475     density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
476     - presently, modify T & S inland (dwnslp_calc_rho.F).
477     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
478     - implementation for ocean in P-coords not tested.
479     - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
480     o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
481 jmc 1.1015 (to facilitate conversion of oceanic pkg to p-coordinate).
482 jmc 1.1014 o change FIND_RHO to FIND_RHO_2D :
483     pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
484     o new pkg: cheapaml
485    
486 jmc 1.1013 checkpoint61b
487 jmc 1.1011 o exch2:
488 jmc 1.1012 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
489     - no longer depend on the order sequence (N,S,E,W).
490     - 3rd exchange no longer needed (tested with 24 tiles).
491     - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
492     - exch_UV_A-grid readily available (but not yet tested).
493     comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
494     (both are no longer needed) in exch_uv: no effect in forward run; but
495     get truncation error differences with adjoint exch.
496     o exch2:
497 jmc 1.1011 - change index-bounds storage (moved from target to local tile,
498     more intuitive this way) ; rename/remove some variables.
499 jmc 1.1012 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
500 jmc 1.1011
501 jmc 1.1010 checkpoint61a
502 jmc 1.1009 o exch2/matlab-topology-generator:
503     fix bug in index bounds for N-S internal exchange (hard to tell if this
504     had any effect on the solution).
505 mlosch 1.1008 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
506     is exceeded
507 mlosch 1.1007 o testreport: modify syntax of awk, so that it works also with
508     awk, and not only with nawk and gawk
509    
510 heimbach 1.1006 checkpoint61
511 heimbach 1.1005 o autodiff
512     Change default for TAF usage by removing argument '-nonew_arg'
513     This changes TAF subroutine argument list (ordering of active var.)
514     Omission of this flag leads to incompatibility w.r.t. TAMC
515     To restore TAMC-compatibility, need following modifs:
516     * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
517     * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
518     Tested TAF version is 1.9.22
519     N.B.: exch2 hand-written adjoint code currently not TAMC compatible
520    
521 heimbach 1.1004 checkpoint60
522     --->>> This is the last checkpoint for which generating the adjoint
523     --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
524     --->>> by default.
525     --->>> Future checkpoints will ommit this flag by default.
526 jmc 1.1003 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
527 gforget 1.1002 o pkg/grdchk: Add gradient check to etan0 perturbations.
528 gforget 1.1001 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
529 gforget 1.1000 o pkg/autodiff: more flexibility in zeroadj.
530     model/src: modifying do_oceanic_phys.F accordingly.
531 gforget 1.999 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
532     o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
533     special setup of gmredi for which the adjoint is stable
534     enough for parameter optimization.
535 gforget 1.998 o bridging the gap between eddy stress and GM.
536     -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
537     along with a change in CPP option (now ALLOW_EDDYPSI).
538     -> when using GM w/ GM_AdvForm:
539     The total eddy streamfunction (Psi = eddyPsi + K x Slope)
540     is applied either in the tracer Eq. or in momentum Eq.
541     depending on data.gmredi (intro. GM_InMomAsStress).
542     -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
543     The key modifications are in model/src/taueddy_external_forcing.F
544     pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
545 jmc 1.1003
546 jmc 1.997 checkpoint59r
547 jmc 1.996 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
548     from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
549     fix option to read coriolis(@ cell-corner) from files with CS-grid.
550 mlosch 1.995 o pkg/mnc: add some attributes to standard 1D-coordinate variables
551 mlosch 1.993 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
552     mass points, when using mnc for output
553     - add runtime parameter (missing_value, missing_value_int) to override
554     default (which is the value of getcon('UNDEF'))
555     o pkg/mnc: prepare mnc for the actual use of missing values with the
556     diagnostics package: small fix in mnc_cw_readwrite.template and more
557     initialisation of never used fields
558 mlosch 1.994 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
559     versions
560     o pkg/thsice/thsice_ini_vars.F added default initial values so that
561     thermodynamics sea ice solver does not blow up when some initial fields
562     are missing.
563 jmc 1.991 o move from external_forcing_surf.F to ini_forcing.F
564     the p-coord. hack consisting in using pLoad to set phi0surf ;
565     update output of tutorial_global_oce_in_p (affected @ truncation level).
566 dfer 1.990 o Freshen up a bit hs94.1x64x5, notably:
567 mlosch 1.994 remove rotationPeriod and tRef=5*0. (adjoint only), and add
568     exactConserv=.TRUE.
569 jmc 1.989 o pkg/generic_advdiff:
570     change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
571     applies to files where Temperature & Salinity 2nd Order moments are used.
572 jahn 1.988 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
573     this uses a dynamically allocated internal state data structure
574     (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
575     and requires a fortran 90 compiler
576    
577 jmc 1.987 checkpoint59q
578 jmc 1.986 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
579     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
580 dfer 1.985 o Refresh tutorial_global_oce_biogeo, notably:
581     - change bathymetry (put back seamounts in ACC, use hFacs)
582     - change EOS (POLY3 --> JMD95Z)
583     - use Bryan-Lewis vertical diffusivity
584     - use multidimensional advection
585     - remove old virtual virtual in dic pkg, now done through ptracer pkg
586     - change a couple of parameters in dic pkg
587 gforget 1.984 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
588 mlosch 1.982 o pkg/obcs: change default to OBCSfixTopo = .true.,
589 mlosch 1.983 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
590     - replace "debugMode" with "debugLevel .GE. debLevB"
591 gforget 1.981 o implementation of TAF directives for gchem,cfc,dic
592 jmc 1.980 o remove "exp5" (replaced by tutorial_deep_convection).
593 mlosch 1.979 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
594     this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
595     the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
596 mlosch 1.982 --> changes results in exp4, seaice_obcs
597 jmc 1.980 o tutorial_deep_convection :
598 jmc 1.978 update the set-up and increase resolution and domain size ; start
599     from pseudo initial conditions = output at t=120mn in order to see
600     something happening when running testreport.
601 mlosch 1.976 o pkg/seaice: add os7mp as an advection scheme
602     add check for advection schemes
603 mlosch 1.977 add a flag for restoring T and S underneath sea ice
604 mlosch 1.975 o pkg/my82: add netcdf-support and diagnostics
605 dfer 1.974 o thsice pkg:
606 mlosch 1.979 - Now hsMax limits snow height by turning it into ice following
607 dfer 1.974 flooding scheme (and now conserving energy)
608     - Slight rewriting of the formula in thsice_calc_thick.F
609     - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
610 jmc 1.980 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
611 dfer 1.974
612 jmc 1.973 checkpoint59p
613     o gchem / dic / cfc :
614     - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
615     - add new parameter files: "data.dic" & "data.cfc" ;
616     - various re-arrangement in initialisation & header file ;
617     - fix tutorial_global_oce_biogeo for multi-threaded test.
618     o pkg/dic: test for "pickup_dic" file when restarting ;
619     if no pickup-file, can restart with a re-initialised pH (same as it did
620 jmc 1.972 before) providing pickupStrictlyMatch is set to False.
621 jmc 1.971 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
622     + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
623 jmc 1.970 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
624     and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
625     o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
626     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
627     (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
628 jmc 1.969 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
629     scheme to use for vorticty-term ;
630     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
631     (with default selectVortScheme, return to original discretisation)
632     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
633 mlosch 1.968 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
634 jmc 1.967 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
635     bottom ; only used with variable horizontal viscosity and non-hydrostatic.
636     also fix diagnostics VISCAHW & VISCA4W.
637    
638 jmc 1.966 checkpoint59o
639 jmc 1.965 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
640 mlosch 1.964 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
641     move a few statemens out the main loop into separate loops
642 mlosch 1.962 o pkg/shelfice:
643     - sort out freshwater flux; convert freshwater fluxes to mass fluxes
644     (kg/m^2/s), does not break tests, because in verification/isomip,
645     rhoConstFresh=rhoConst (by accident)
646 mlosch 1.963 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
647     - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
648     new file model/src/seawater.F, so that they are available for all pkgs.
649     - convert potential temperature into in-situ temperature. This changes the
650     isomip tests => update tests
651 mlosch 1.961 o add a flag writePickupAtEnd (default=true) to be able to suppress
652     writing a pickup at the last timestep
653 jmc 1.966 o tools/mpack-1.6 :
654     - disable automake (not working) and autoconf (not needed).
655     - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
656     also cleaner with much less compilation warnings.
657 gforget 1.960 o pkg/profiles:
658     rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
659     (for "less than 32 characters name" compiler requirement)
660 dimitri 1.959 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
661     conditions that have a different sampling frequency than S/T/U/V obcs
662 jmc 1.958 o pkg/diagnostics (stats-diags):
663     - fix global Min/Max in case 1 processor get only empty tiles
664 mlosch 1.957 o genmake2: replace (4 times)
665     make genmake_tc_1.o >> genmake_warnings 2>&1
666     with
667     COMM="$CC $CFLAGS -c genmake_tc_1.c"
668     echo $COMM >> genmake_warnings
669     $COMM >> genmake_warnings 2>&1
670     to make genmake2 always see the value of CC as specified in the optfile.
671 jmc 1.956 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
672     - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
673     - modify verification advect_cs test to test SOM-advection on CS-grid.
674 gforget 1.955 o pkg/ctrl:
675     - Rewrite of ctrl_map_ini_ecco.F,
676     introducing a generic routine (ctrl_map_ini_gen.F).
677     - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
678 jmc 1.956
679 jmc 1.954 checkpoint59n
680 jmc 1.953 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
681     number in dedicate array "hdiag":
682     - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
683     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
684     - many small changes (integer format) for large number of diagnostics
685     - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
686     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
687 mlosch 1.952 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
688     usingSphericalGrid, this allows to define the rotated grid coordinates
689     via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
690     geographical coordinates according to the inverse of the rotation defined
691     by the Euler angles, so that Coriolis parameter and online-interpolation by
692     exf works with the geographical coordinates on XC/YC/XG/YG.
693     Naturally, this feature does not work with all packages, so some
694     combinations are prohibited in config_summary (flt, flt_zonal, ecco,
695     profiles), because there the coordinates are assumed to be regular
696     spherical grid coordinates.
697 gforget 1.951 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
698     - introduce isopycnal diffusion coefficient control.
699     o tools/adjoint_options:
700     - additional control vector components.
701 mlosch 1.950 o pkg/mnc: have mnc create marginally meaning full coordinate variables
702     (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
703 jmc 1.948 o pkg/mypackage:
704     - add example of read/write pickup for state-var ;
705     - add entry points to the main code for state-vars diags & write-pickup.
706 dimitri 1.946 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
707     transitions for useExfYearlyFields
708 mlosch 1.947 - add new subroutine that determines the file to read from for
709     use*YearlyFields = .TRUE. and .FALSE.
710 mlosch 1.949 - add a verification experiment to global_with_exf that tests
711     useExfYearlyFields with USE_EXF_INTERPOLATION defined
712 mlosch 1.945 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
713     analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
714     subroutines (which could be generated from a template, because they are
715     almost identical), for now they are included in obcs_prescribe_read.F for
716     simplicity
717 mlosch 1.943 o pkg/exf:
718     - add a little more diagnostic to exf_interp_read (in analogy to
719     mds_read_field, can be turned off with debugLevel < debugLevA=1)
720     - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
721 mlosch 1.944 ugly but fast by unrolling short inner loops, inserting a unroll=8
722     directive in routine lagran, and splitting a loop and making do while the
723     outermost loop (the latter requires the intoduction of index arrays)
724 dimitri 1.942 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
725 dimitri 1.941 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
726     http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
727 dimitri 1.940 o verification/seaice_obcs: updated for restart test and latest options
728 mlosch 1.939 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
729     ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
730     for now this is only available for the C-grid code and also within
731     #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
732    
733 jmc 1.938 checkpoint59m
734 dimitri 1.936 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
735     and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
736 dimitri 1.937 o gad_som : fix flux output (& diagnostics) to have same units as other
737     advection scheme fluxes (was previously multiplied by deltaT).
738 dimitri 1.933 o added verification/seaice_obcs both to test seaice open boundaries
739     and to provide an example matlab scrpt for generating them
740     o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
741 atn 1.931 o pkg/salt_plume: clean up salt_plume_frac.F to
742     remove redundancy in PlumeMethod 1 and 4
743 atn 1.930 o pkg/kpp: added saltplume diagnostics
744 dimitri 1.929 o pkg/obcs and pkg/seaice:
745     - do not set uice and vice to zero when OB*icefile are unspecified
746     - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
747     - moved seaice tracer obcs after call to seaice_growth
748 dimitri 1.927 o pkg/salt_plume: added various options for salt plume depth
749     criterion and for vertical distribution of the salt
750 jmc 1.928
751     checkpoint59l
752 jmc 1.925 o pkg/ptracers: new version of ptracers pickup:
753     read meta file and write only fields which are needed to restart.
754     ( same logic as main pickup file ; also using pickupStrictlyMatch )
755 dimitri 1.924 o pkg/seaice:
756 mlosch 1.923 - add timescale for melting due to warm mixed layer as a means of
757     setting SEAICE_availHeatFrac more conveniently
758     - add a CPP-flag/runtime parameter check for flooding algorithm
759 dimitri 1.924 - reformulated availHeat in seaice_growth.F to be independent of AREA
760 mlosch 1.923 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
761     unit changes
762 dimitri 1.921 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
763 mlosch 1.919 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
764     SX vector computer.
765 dimitri 1.920 o pkg/seaice:
766     - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
767     seaice forcing fields can now be read only through pkg/exf
768     - removed some unused halos
769 jmc 1.917 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
770 dimitri 1.922 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
771     or U/VICE from U/VWIND before computing U/VSTRESS
772 dimitri 1.916
773 jmc 1.915 checkpoint59k
774 dimitri 1.914 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
775     dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
776 jmc 1.913 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
777 jmc 1.925 all experiments pass when compile with un-initialised var. checking option.
778 dimitri 1.912 o added pkg/salt_plume
779 jmc 1.911 o script to test restart (for now, in MITgcm_contrib/jmc_script)
780     o pkg/seaice: new read/write pickup version.
781     read meta file and write only fields which are needed to restart.
782     ( same logic as main pickup file ; also using pickupStrictlyMatch )
783 mlosch 1.910 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
784 jmc 1.909 o lab_sea.hb87: modify the domain & update output.hb87.txt :
785     lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
786     at j=1 & j=Ny+1 : this case is not treated correctly in the restart
787     process. Fixed here by closing the domain at the Northern boundary.
788     o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
789     o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
790     a set of consecutive levels in/from a 3-D array.
791 jmc 1.908 o pkg/ptracers:
792 jmc 1.909 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
793 jmc 1.908 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
794    
795 jmc 1.907 checkpoint59j
796 jmc 1.906 o in pkgs: dic, obcs, offline, rbcs:
797     standard way to compute coeff. for time interpolation between 2 time reccords
798     which retains full precision (& make results less dependent on compiler).
799     update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
800 mlosch 1.905 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
801     packages instead of reading ice cover and wind speed separately
802 jmc 1.904 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
803     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
804     to allow to compile customized code before the update)
805 jmc 1.903 o cleaning-up:
806     - fix CPP instruction syntax in pkg/obcs
807     - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
808     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
809     - fix some threads issue in IO parts.
810 dfer 1.901 o pkg/dic:
811     - add tons of "_d 0" (--> much better testreports !)
812     and then update outputs of tutorial_global_oce_biogeo
813 jmc 1.900 o pkg/mom_fluxform:
814     add a special version of momentum advection intended to conserve momentum
815     next to a bathymetry step or a coastline edge. (default = off = #undef)
816 jmc 1.898 o new read/write pickup version:
817     - for now, only implemented for main (mdsio) pickup file.
818     - write out only what is needed to restart; merge pickup_nh , pickup_ph
819     and main pickup together.
820     - read meta file; read only what is needed to restart; stop if a field
821     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
822     if it make sense (even if the restart is not perfect).
823     - if no meta file, assume that pickup to read corresponds exactly to
824     a pickup that would currently be written.
825     - read pickup written in the old format (until checkpoint59i) if it
826     recognizes an old meta file (no field-list).
827     - add a meta file in exp. which starts from a pickup: 2 cases:
828     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
829     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
830     b) a meta file describing the content of the associated pickup file
831     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
832     o pkg/mdsio & pkg/rw:
833     - new routine to read a meta file ; new set of routine to read
834     Multiple-fields file (with meta file).
835 dimitri 1.899 o added open boundary conditions capability for seaice
836     HSNOW, HSALT, UICE, and VICE
837 dimitri 1.897
838 jmc 1.896 checkpoint59i
839 heimbach 1.895 o adjoint:
840     * fix multiDimAdvection adjoint
841     (partial recomputation problem by TAF for fVerT(:,:,kDown)
842     and comlev1 size definition (maxpass vs. max. number of tracers)
843     * verification/global_ocean.90x45x15 adjoint now tests
844     NLFS and multiDimAdvection using DST3 (=30)
845     * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
846 jmc 1.894 o pkg/kpp: add "_d 0" to real constant (if missing);
847     update output of exp: natl_box (10.digits); vermix (std, 7.digits)
848     and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
849 jmc 1.893 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
850     for internal parameters related to restart process (formerly from PARAMS.h)
851     and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
852     o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
853     as argument. (only atm2d & obcs write_pickup have not yet been updated)
854 jmc 1.892 o pkg/monitor:
855     - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
856     - fix mon_stats_rs (statistics over the full domain, even where field is zero)
857     - account for deep Atmosphere factor and density factor (anelastic)
858 dimitri 1.891 o added open boundary conditions capability for seaice HEFF and AREA
859 mlosch 1.890 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
860     thermodynamics
861     - requires a little reorganization, which affects the testreport results
862     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
863     so that now the conservative form is tested
864     - add a few comments
865 jmc 1.892 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
866 mlosch 1.888 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
867 mlosch 1.887 o add new diagnostics to seaice: advective, diffusive fluxes (only for
868     multidim-advection, for scheme 2 they are not filled) and transports,
869     thermodynamic growth rates
870 jmc 1.902 o change units of EmPmR (inside the code, + within coupling interface)
871     from m/s to kg/m2/s (mass flux) but leave input file unchanged.
872     Affects results @ truncation level (cg2d match) and update output of
873     experiments: lab_sea(6), global_ocean.90x40x15(10),
874 jmc 1.886 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
875     + adjoint results: global_ocean_ebm(11) and lab_sea (12).
876 jmc 1.902 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
877 jmc 1.886 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
878    
879 jmc 1.885 checkpoint59h
880 mlosch 1.884 o pkg/exf:
881     - improve vectorization by moving if-statement out of loops in
882     exf_mapfields, exf_radiation
883     - exf_bulkformulae.F: introduce 2D fields and vectorize code
884 dimitri 1.881 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
885 jmc 1.880 o testreport:
886     - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
887     monitor & update offline_exf_seaice exp. output.
888     - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
889 mlosch 1.879 o pkg/seaice:
890     - bug fix in the evp solver: boundary conditions were affected be
891     masking of zMax/zMin (changes results)
892     - minor bug fix in boundary conditions in seaice_calc_strainrates
893     (changes results for no_slip)
894     - seaice_lsr.F: make interpolation of eta dependent on boundaries
895     - replace hardcoded lower limit for zeta (zMin) by runtime parameter
896     - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
897     stress formulation and no-slip boundary conditions
898 jmc 1.878 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
899     in gad_calc_rhs.F ; add few safety stops in initialisation phase.
900 dimitri 1.877 o pkg/seaice: a first HSALT time stepping equation has been checked in
901 dimitri 1.875 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
902     in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
903     without requiring DO-IF statements
904 jmc 1.876 o pkg/thsice:
905     use continuous power-law function for partition of energy between lateral
906     melting/freezing and thinning/thickening ; old code using step function
907     still available with #undef THSICE_FRACEN_POWERLAW
908     update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
909     o testreport: change AD testing : check against results/output_adm.txt
910     using same scripts as for forward test.
911 dimitri 1.875
912 jmc 1.874 checkpoint59g
913 jmc 1.873 o adjoint testing: in preparation for changing testreport:
914     - output format: cost and grad written on separated lines
915     - ad output results in directory "results" (instead of "results_ad")
916 dimitri 1.872 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
917 dimitri 1.871 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
918 gforget 1.870 o pkg/ecco: allow user defined cost function contributions
919 jmc 1.869 o testreport:
920     Allow to choose (per experiment) the list of tested output variables
921     and the main variable (used to issue a pass/FAIL ) ;
922     - for now, done by adding the specific list in file: [exp]/input/tr_checklist
923 jmc 1.873 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
924 jmc 1.869 Also modify printing of summary:
925     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
926     b) echo the list of tested variables in the individual summary.txt of
927     each experiment.
928 jmc 1.868 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
929     threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
930     (but still depend on the tile decompostion of the domain).
931 mlosch 1.867 o pkg/seaice: change a discretization detail to make the B-grid code
932     "more symmetric". This change is likely to remove all "ridges/leads" that
933     where quasi-aligned with the grid in B-grid solutions. It may also be
934     the solution to the stress coupling issues with the B-grid.
935 jmc 1.866 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
936     remove .cvsignore from input dir. (since testreport no longer run here).
937 jmc 1.865 o pkg/thsice:
938 jmc 1.866 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
939 jmc 1.865 - fix reshaping of sea-ice just after advection:
940     melt all the ice only if ice-volume is too small.
941     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
942     prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
943     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
944 jmc 1.864 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
945     tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
946 jmc 1.863 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
947     forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
948     (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
949     and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
950     of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
951     -> update output.txt
952     o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
953     this affects truncation error: -> update output.txt of exp:
954     global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
955     ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
956    
957 jmc 1.862 checkpoint59f
958 gforget 1.861 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
959     o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
960     a bounded range (in forward mode)
961 gforget 1.860 o pkg/ecco, ctrl, autodiff and mom_common:
962     internal parameter controls, completements of implementations
963 jmc 1.859 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
964 jmc 1.862 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
965     (not seem any difference in testing results).
966 jmc 1.859 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
967     at face corners.
968 jmc 1.858 o pkg/generic_advdiff:
969     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
970     loop range indices for computing vertical advection tendency
971     and do the calculation in the interior only (no overlap) ;
972     for now, only implemented for SOM advection (to save CPU time).
973     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
974 heimbach 1.855 o exch2 adjoint
975     First set of changes:
976     - add exch2 hand-written adjoint templates
977     - exch2 hand-written no longer use TAF-flag 'nownew_arg'
978     This will require cleanup in pkg/autodiff/*.F
979     (changed routines currently kept separate in verif. code/)
980     - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
981     that used to hide exch2 or cubed-sphere specific code
982     (commented via 'cph-exch2')
983 dimitri 1.856 o pkg/seaice
984     - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
985 jmc 1.857 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
986     output of global_ocean.cs32x15.thsice .
987 heimbach 1.855
988 jmc 1.854 checkpoint59e
989 jmc 1.853 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
990     for B-grid vector (not yet tested) and C-grid vector (<- only used
991     when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
992 dimitri 1.852 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
993     (#ifdef ALLOW_SALT_PLUME)
994 dimitri 1.851 o gather_2d/scatter_2d: removed halo regions
995 jmc 1.845 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
996     scheme and the corresponding test case (under front_relax dir). For now,
997     only available with Skew-flux form and not yet tested in realistic set-up.
998 heimbach 1.847 adjoint: store directives updated, but gradient checks deteriorated,
999     so maybe GM/Redi adjoint is now broken.
1000 heimbach 1.844 o seaice adjoint
1001     * add AREA, HEFF, HSNOW as control variable
1002     (should not change lab_sea results)
1003     * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1004 dimitri 1.848 o pkg/seaice:
1005     * added computation of saltFlux in seaice_growth;
1006     For time being, sea ice salinity is assumed constant
1007     contribution of snow flooding to freshening of sea ice is neglected.
1008     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1009     defaults to 0.0 in order to maintain backward compatibility.
1010     Typical values for SEAICE_salinity are 4 to 10 g/kg.
1011     * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1012     * added SEAICE_availHeatFrac, which specifies fraction of surface level
1013     heat content used to melt or grow ice
1014 dimitri 1.849 * commented out cap of HICE: it helps keep ice thinner
1015     * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1016 dimitri 1.850 * applied OBCS T/S mask to HEFFM sea ice mask
1017 heimbach 1.844
1018 jmc 1.843 checkpoint59d
1019 jmc 1.842 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1020     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1021     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1022     o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1023     and change default value of parameter "GM_Small_Number";
1024     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1025     global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
1026     tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1027 gforget 1.841 o pkg/ecco: cost function when applying pkg/smooth to controls
1028     o pkg/ctrl: add forcingPrecond run time parameter
1029 mlosch 1.839 o pkg/seaice:
1030     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1031     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1032     changes verification/lab_sea
1033     - rearrange implicit part of u-equation in LSR solver to make it easier to
1034     read, understand, and debug. This causes changes at the truncation level.
1035     - fix (serious) bug in the boundary conditions (sign error in the implicit
1036     part) of the LSR solver. Changes all LSR results.
1037 dimitri 1.840 - fixed problem with HSNOW initialization to avoid thick snow when AREA
1038     is initilized with small values - does not change lab_sea results.
1039     - added HsnowFile initialization capability
1040 gforget 1.838 o pkg/smooth: addition to model/src and pkg/ctrl so allow
1041     initialization of pkg/smooth and application to control vector
1042 mlosch 1.837 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1043 gforget 1.836 o dependencies: pkg/profiles requires pkg/cal
1044 gforget 1.835 o pkg/profiles:
1045     - added option ALLOW_PROFILES_GENERICGRID
1046     -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1047     that interpolation information (grid points and coefficients) is provided
1048     within the netcdf input files.
1049     -> sample matlab scripts can be found in MITgcm_contrib/gael
1050     that allow you to prepare netcdf input files.
1051     - also modified: cleaner include statements, cleaner error print statements,
1052     cleaner stops when error, and more tests of the netcdf input files consistency.
1053 jmc 1.834 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1054 mlosch 1.830 o pkg/seaice:
1055 mlosch 1.833 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1056     requires a new routine: seaice_diagnostics_fill.F
1057 mlosch 1.832 - make sure that seaice does not move if not forced (pressure replacement
1058     method, Hibler and Ip, 1995), changes results
1059 mlosch 1.830 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1060     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1061     It is turned off by default (=-1.), because it changes the results.
1062 mlosch 1.831 - make it possible to read AREA from a file, too.
1063 mlosch 1.830
1064 jmc 1.829 checkpoint59c
1065 jmc 1.828 o add S/R and diagnostics for oceanic mixed-layer depth
1066     o move GMRedi call after all vertical mixing schemes (including KPP)
1067     o pkg/thsice:
1068     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1069     (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1070 mlosch 1.824 o pkg/obcs:
1071     - bug fix for balance code
1072 mlosch 1.822 o pkg/seaice:
1073 mlosch 1.825 - allow values of SEAICE_elasticParm > 1
1074 mlosch 1.826 - add new parameter SEAICE_evpTauRelax as an alternative
1075     to SEAICE_elasticParm
1076 mlosch 1.825 - make lsr boundary conditions free slip (by default), changes result
1077 mlosch 1.823 - add code for no slip boundary conditions for lsr
1078 mlosch 1.822 - set minimum of zeta to zero (and not 4e8) (changes results)
1079 mlosch 1.826 - add a cap on AREA after advecting AREA if seaice_growth is not called
1080 jmc 1.821 o change calculation of Visbeck K:
1081     - no longer depend on tapering scheme; instead, compute slope (limited
1082     by GM_maxSlope). this is equivalent to what was comuted before with
1083     clipping or linear tappering.
1084 jmc 1.828 - fix vertical averaging (wrong by 1/2 level)
1085 jmc 1.821 - leave the old version (but will not be maintained) within
1086     #ifdef OLD_VISBECK_CALC / #endif
1087 jmc 1.828 - update output of exp. ideal_2D_oce
1088 mlosch 1.820 o change error catch in calc_r_star to improve vectorization
1089 jmc 1.819 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1090     add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1091 heimbach 1.827 o adjoint:
1092     Re-organized adjoint checkpointing according to Matt Mazloff
1093     (but with modifs/completions/cleanups)
1094     Storing is now bundled into large arrays to optimized I/O
1095     (and second step in cleanup of the_main_loop)
1096 jmc 1.819
1097 jmc 1.818 checkpoint59b
1098     o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1099     - export/import (between ocean & coupler) fields needed for ocean DIC.
1100 mlosch 1.817 o pkg/seaice:
1101     - get rid of three more exchanges seaice_calc_viscosities (required
1102     different loop boundaries in seaice_lsr and seaice_ocean_stress)
1103     - bug fix in seaice_ocean_stress (update of lab_sea required)
1104     - reduce loop boundaries to necessary minimum also in seaice_evp
1105     - go back to the old way of computing deltaC/Z as the adjoint likes that
1106     better
1107 dfer 1.816 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
1108     passive tracer to an Age Tracer) + update output.txt
1109 jmc 1.814 o pkg/exf:
1110 jmc 1.815 - implement A-grid / C-grid selection for wind-stress input files.
1111     - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
1112     for now, in exf_bulk_largeyeager04.F only :
1113     - change implementation for case where windspeed + 2. components wind-stress
1114     are read-in. AND use rhoConstFresh to convert evap.
1115     o pkg/seaice:
1116     - use correct EXCH_UV for wind-forcing (on A-grid).
1117     - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
1118     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
1119     o pkg/exf:
1120 jmc 1.814 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
1121     EXF_INTERPOLATION:
1122     - merge global_with_exf/code version of exf_interp_read.F
1123     to the main code ;
1124     - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
1125     reading the file ; Important: This options needs to be defined to recover
1126     previous code.
1127     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
1128     - no longer loose real*8 precision along the way when using exf_iprec=64.
1129 mlosch 1.811 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
1130 mlosch 1.813 - change discretisation of evp-solver in order to avoid another exchange
1131     (changes lab_sea) and clean up a little
1132     - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
1133     help the adjoint (this also changes the results slightly)
1134     - add a few "_d 0" where they had been missing in seaice_evp.F
1135     - cleaning up: remove unused seaice_calc_rhs.F
1136 jmc 1.810 o pkg/exf: some cleaning-up:
1137     - change various "constants" into runtime parameters
1138     - cleaned-up Large&Yeager04 routine which should eventually
1139     replace exf_bulkformulae.F (changed names of S/R and CPP)
1140     and merged various ALLOW_ATM_WIND options
1141     only used with thsice pkg (in thsice_get_exf.F):
1142     - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
1143     which are used when useStabilityFct_overIce=TRUE (= the default)
1144     - change default values of ice & snow emissivity and scale downward LW
1145     by ice & snow emissivity.
1146     o pkg/thsice:
1147 jmc 1.809 fix few little problems, in thsice_calc_thickn.F:
1148     - growth vertically (and not laterally) if iceFrac == iceMaskMax
1149 jmc 1.828 - melt only laterally if hIce < hThinIce (as the comments say)
1150 jmc 1.809 and in thsice_extend.F:
1151     - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1152     - start to form ice as soon as the minimum ice-volume is reachable.
1153     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
1154     and cpl_aim+ocn
1155 mlosch 1.807 o pkg/kpp
1156 jmc 1.809 - move computation of surface related input fields to KPP into a new
1157     subroutine kpp_forcing_surf.F
1158 jmc 1.808 - remove wrong (within bi,bj loops) EXCH calls.
1159     - little cleaning (add argument myThid in last position, cvs header ...)
1160 jmc 1.809 - for now, fix conservation problem by exchanging KPPviscAz (may not
1161     be the best fix)
1162 mlosch 1.806 o pkg/seaice
1163     - check for inconsistent evp parameter/cpp-flag combination
1164     - remove leftover errIO flat for obsolete name list error handling
1165 heimbach 1.812 o OpenAD
1166     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1167 mlosch 1.806
1168 jmc 1.805 checkpoint59a
1169 mlosch 1.803 o pkg/seaice: some parameter clarifications and a little bit of clean up
1170 jmc 1.802 o pkg/thsice: rename run-time parameters:
1171     himin -> hIceMin
1172     himin0 -> hThinIce
1173     hihig -> hThickIce
1174     i0 -> i0swFrac
1175     transCoef -> bMeltCoef
1176     frac_energy -> fracMelting
1177     add new parameters: hNewIceMax, fracFreezing, dhSnowLin
1178     with default values (for now) that do not change the results.
1179     remove old version of thsice vars advection in pkg/seaice.
1180 jmc 1.801 o in FFIELDS.h:
1181     - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
1182     - make pLoad & sIceLoad always available (but still only used if
1183     ATMOSPHERIC_LOADING is #define).
1184 dimitri 1.799 o pkg/kpp: replaced _KPP_RL with _RL
1185 dimitri 1.798 o bug fixes for vertical diffusivity computations when both KPP and
1186 dimitri 1.883 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1187     are no longer updating the vertical diffusivity array
1188     (passed as argument) but are (re-) setting those arrays.
1189 mlosch 1.795 o pkg/seaice: fix bug in evp solver, while doing that
1190     - change (improve?) discretization of stress computations for both
1191     cgrid-lsr and evp solver
1192     - add a new routine to compute strain rates
1193 mlosch 1.796 - the above changes lab_sea results
1194     - add no slip conditions for evp solver (off by default), lsr-version
1195     may follow
1196     - fix exchange for shear at Z-points (does not change lab_sea)
1197     - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
1198     (to force the user to pick a time step since there is not "safe" way
1199     of choosing it)
1200 mlosch 1.797 - add principal stress diagnostics
1201 mlosch 1.800 - rearrange fields for evp a little to avoid having to call a: too many
1202     exchanges and b: exchanges for stress trensor components which we do
1203     not have.
1204     - modify Hibler+Bryan (1987) stress coupling so that it reuses information
1205     of evp, complete rewrite for lsr case (latter is does not yet work
1206     in all cases)
1207 mlosch 1.794 o pkg/kpp: add code to have mixing in shelf ice caverns
1208 mlosch 1.804 - add myThid to all kpp routines (long overdue)
1209 mlosch 1.794
1210 heimbach 1.793 checkpoint59
1211 heimbach 1.792 o pkg/exf:
1212     - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
1213     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
1214     - move exf header files from lower_case.h to UPPER_CASE.h ;
1215     add missing cvs Header & Name
1216     - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
1217 heimbach 1.793 - add namelist param. selectStressGridPosition, exf_monFreq
1218     - retire many _CLIM routines, and remove data.exf_clim
1219     + params moved to data.exf
1220     + climsst, climsss now handled by exf_set_gen, i.e.
1221     climss?period=0 refers to constant field,
1222     climss?period=-12 to monthly forcing
1223     - split up namelists in data.exf
1224 mlosch 1.788 o pkg/seaice:
1225     - remove seaice_exch and seaice_exch_uv
1226     - remove superfluous exchange of theta
1227     - add myThid to seaice_budget_ocean/ice
1228 mlosch 1.790 - add new interface for atmospheric wind forcing (C-grid only)
1229     + new routine
1230     + two new field (taux, tauy for stress over ice)
1231     + removed one global field (DAIRN) for C-grid case only
1232 heimbach 1.792 o pkg/thsise
1233     - 2nd set of modifs for thsice adjoint in conjunction with exf
1234 heimbach 1.793 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
1235 mlosch 1.788
1236 jmc 1.787 checkpoint58y_post
1237 dimitri 1.785 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
1238 dimitri 1.786 vertical diffusivity, similar to that in MOM4; turned on using
1239     #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
1240     diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
1241 dimitri 1.782 o Added capability for 3D specification of background vertical diffusion
1242     coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
1243     in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
1244     "data" file that contains the 3D vertical diffusivity coefficients.
1245 jmc 1.784 o ice dynamics (pkg/seaice) with thsice thermodynamics:
1246     - add code within pkg thsice to advect & diffuse sea-ice fields
1247     similar to (and will replace) what has been added in seaice_advdiff.F,
1248     but: - conserving Mass, Heat & Salt.
1249     - better when using non-linear advection scheme (not yet fully tested)
1250     - can also be used in atmospheric set-up (for now, only the diffusion).
1251 dimitri 1.783
1252 jmc 1.780 checkpoint58x_post
1253 jmc 1.779 o IO option for global-file compact format:
1254     - add options when generating topology (utils/exch2/matlab-topology-generator)
1255     - add I/O capability (pkg/mdsio).
1256     - adapt utils/matlab/rdmds.m to read this format.
1257     for now long-line format not yet supported by pkg/mdsio (& exch2).
1258 mlosch 1.778 o shelfice: add a few diagnostics
1259    
1260 jmc 1.777 checkpoint58w_post
1261 jmc 1.776 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
1262     rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
1263     (and replace horiVertRatio in NH code).
1264     Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
1265     and tutorial_plume_on_slope (sensitive to truncation)
1266 mlosch 1.774 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
1267     directly to drive seaice model (C-grid only)
1268     o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
1269     - reintroduce computation of wind from stress,
1270     - compute tau (in exf_bulkformulae.F) from windstress averaged to
1271     mass points to avoid tau = 0
1272 mlosch 1.775 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
1273 mlosch 1.774 o rdmnc.m: make it work with "global" files created with gluemnc
1274 jmc 1.773 o rdmnc.m : some improvements in dealing with singleton dimension
1275     (tested on all testreport mnc output files).
1276     o genmake2: disable pkg/profiles if netcdf test fails.
1277 jmc 1.772 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
1278 mlosch 1.771 o move call to cal_readparms up to make calendar parameters/variable available
1279     to all packages
1280    
1281 jmc 1.770 checkpoint58v_post
1282     o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
1283     useDynP_inEos_Zc tested.
1284 dimitri 1.769 o pkg/exf: changes to properly interpolate/mask/scale initial fields
1285 dimitri 1.768 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1286     and portions thereof. See read_cs.txt for description and examples.
1287 jmc 1.767 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1288     add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1289     following the great-circle arc between those 2 points.
1290     o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1291     (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1292 jmc 1.766 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1293     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1294     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1295     - still needs work (not working with some options ; efficiency to improve)
1296     and serious testing.
1297     - use this scheme for temperature & salinity in 2 advection test exp.:
1298     advect_xy & advect_xz, respectively.
1299    
1300 jmc 1.765 checkpoint58u_post
1301     o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1302 jmc 1.764 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1303     o testreport: add option "-skipdir" to skip some test.
1304     o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1305     momentum calculation.
1306     o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1307     o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1308     remove checkpoint.F and the_correction_step.F (no longer used);
1309     do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1310     o add option (linFSConserveTr) to correct for tracer source/sink due to
1311     Linear Free surface
1312 mlosch 1.763 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1313     o pkg/thsice: fix reading mnc-pickups
1314    
1315 jmc 1.762 checkpoint58t_post
1316 jmc 1.761 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1317     o pkg/mdsio:
1318     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1319     move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1320     mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1321     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1322     - collect old S/R in one file: mdsio_rw_field.F (now just a call to
1323     either MDS_READ_FIELD or MDS_WRITE_FIELD )
1324     - new S/R (to replace MDSWRITEMETA), which allows to write more
1325     informations (variable names, time ...) to meta files.
1326     - modify rdmds.m to give back the meta file content.
1327 jmc 1.760 o pkg/diagnostics: change vertical interpolation to be safer, and more
1328     flexible (define p-levels to interpolate to in data.diagnostics);
1329     add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1330     diagnostic pointer.
1331 mlosch 1.759 o pkg/seaice: more cleaning up of seaice_growth, added many comments
1332 mlosch 1.763 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1333 mlosch 1.757 o fix multi-category seaice:
1334     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1335     SEAICE_MULTICATEGORY
1336     - fix short wave heat flux
1337 jmc 1.758 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1338     and allow to use EVP solver. Change forward lab_sea: test both EVP
1339     solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1340 heimbach 1.756 o Initial check-in of lab_sea adjoint
1341     (very similar to natl_box_adjoint/code_seaice)
1342     * used C-grid and EVP solver
1343     * used KPP, GM/Redi
1344     * uses inAdExact=.TRUE.
1345     * gradient checks fail for both ADM and TLM
1346     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1347     f.d. gradients actually seem more problematic than ADM, TLM gradients;
1348     issue is related to forward mismatch between g77 an ifort
1349 mlosch 1.755 o pkg/seaice: overhaul of thermodynamics
1350     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1351     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1352     - move a few global fields out of SEAICE.h into seaice_growth.F and
1353     make them 2D (FICE/QNETO/ ...)
1354     - remove FO (it is the same as QNETO)
1355     - introduce a few local fields to avoid modifying external fields such
1356     as atemp, etc.
1357    
1358 mlosch 1.754 checkpoint58s_post
1359 dimitri 1.753 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1360     changed exf_set_gen.F so that
1361     genperiod=0 means input file is one time-constant field and
1362     genperiod=-12 means input file contains 12 monthly means
1363 jmc 1.752 o CG2D: use pre-computed solver main-diagonal (stored in common block);
1364     this affects truncation error ; generate new output file for exp. which
1365     fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1366     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1367     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1368     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1369     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1370     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1371 jmc 1.751 o start implementation of deep-atmosphere and anelastic formulation
1372 jmc 1.750 o verification: remove 2nd copy of input files and use script "prepare_run"
1373     to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1374 mlosch 1.749 o mom_common/vecinv/fluxform: fix a few initialisation isssues
1375 gforget 1.748 o profiles: fix for multithreaded case
1376    
1377 jmc 1.746 o diagnostics: rename few diags:
1378     s/'PRESSURE'/'RCENTER '/g
1379     s/'TICE '/'oceFreez'/g
1380     s/'TAUX '/'oceTAUX '/g
1381     s/'TAUY '/'oceTAUY '/g
1382     s/'SWFLUX '/'oceQsw '/g
1383     s/DIFx/DFxE/g
1384     s/DIFy/DFyE/g
1385     and add few ocean-forcing diagnostics:
1386     atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1387 dimitri 1.747 o modifications to pkg/seaice/growth.F and budget.F, which change results of
1388     lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1389     as actual snow thickness. It now refers everywhere to effective snow
1390     thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1391 jmc 1.746
1392 jmc 1.745 checkpoint58r_post
1393 dimitri 1.744 o modifications to pkg/seaice/growth.F, which change results of
1394     lab_sea experiment: fixes pertain to melting snow over open water, to
1395     masking EVAP under sea ice, and to using the correct AREA variable for
1396     computations of EVAP, PRECIP, HSNOW, and GHEFF
1397 edhill 1.743 o add ability to read bathy, salt, and theta using MNC (off by def)
1398 mlosch 1.742 o add flooding algorithm and advection of HSNOW for pkg/seaice;
1399     both are turned off by default and do no change any results
1400 jmc 1.741 o seaice advection with pkg/thsice: a step toward the use of non-linear
1401     advection scheme, but #ifdef or commented out for now (requires more EXCH).
1402 jmc 1.739 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1403     (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1404     in natl_box (affects results @ truncation level: update output.txt)
1405     o multi-threading and IO:
1406 jmc 1.738 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1407     - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1408     (needed to work with SingleCpuIO): tested in all verif. exp.
1409 jmc 1.737 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1410     affects the results (but none of the verification test uses this scheme).
1411 heimbach 1.736 o Adding some pkg/diagnostics capability to pkg/seaice
1412     (will certainly be subject to changes)
1413 heimbach 1.740 o ctrl: adding new control variables:
1414     lwflux, lwdown, evap, snowprecip, apressure, runoff
1415 heimbach 1.736
1416 jmc 1.735 checkpoint58q_post
1417 dimitri 1.734 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
1418     1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1419     high_res_cube configuration by 4% on Columbia.
1420 jmc 1.733 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1421     add (in global_with_exf/code) a version of EXF_INTERP_READ without
1422     dynamical allocation (seems to work in multi-threaded).
1423     o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1424     single CPU io) so that TAF does not have to see EESUPPORT.h
1425 jmc 1.727 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1426    
1427 heimbach 1.725 checkpoint58p_post
1428 mlosch 1.726 o obcs: stop if obcs is used with useCDscheme = .true.
1429 mlosch 1.723 o shelfice:
1430     - fix a sign error so that no slip at shelfice interface works
1431     - remove stop for combination non-hydrostatic code and shelfice. That does
1432     not mean, that the results are correct, but at least they are numerically
1433     stable
1434 dfer 1.721 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1435 heimbach 1.724 o added adjoint exch routined for all exch*3d* routines
1436     and updated flow directives
1437 dfer 1.721
1438 jmc 1.720 checkpoint58o_post
1439     o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1440     remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1441 jmc 1.719 o change controling S/R for writing pickup file (new S/R do_write_pickup)
1442     and clean-up reading/writing of pickup files.
1443     o fix local version of read/write pickup (NH part) in rotating_tank/code
1444 jmc 1.718 o simplify EXCH interface:
1445     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1446     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1447 edhill 1.717 o added the regrid package
1448 mlosch 1.716 o shelfice:
1449     - add a simple boundary layer scheme to reduce noise
1450     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1451 jmc 1.718
1452 jmc 1.714 checkpoint58n_post
1453 jmc 1.713 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1454     local variable (not in common block).
1455 jmc 1.712 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1456     - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1457     - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1458     to work with SingleCpuIO.
1459 jmc 1.711 o add "_d 0" to real constant of pkg/cfc subroutines ;
1460     update exp. cfc_exemple & tutorial_cfc_offline output files.
1461 jmc 1.710 o multi-threading and IO:
1462     - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1463     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1464     - barrier before and after reading.
1465     - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1466     - avoid using MDS_WRITELOCAL for LAND pkg output.
1467     - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1468     common-block variables ; Allows multi-threading with master-thread IO.
1469 jmc 1.709 o change default MAX_NO_THREADS from 32 to 4 ;
1470     and stop cleanly when MAX_NO_THREADS is too small.
1471     o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1472    
1473 jmc 1.708 checkpoint58m_post
1474 jmc 1.707 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1475     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1476 jmc 1.706 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1477     keep global_ocean.90x40x15 (for AD testing) with former secondary test
1478     (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1479     o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1480     add MITgcm_tutorials (= code + all the tutorials)
1481 gforget 1.705 o ecco, option to compute cost for total ssh (mean+anom)
1482 gforget 1.704 o consistent with addition of ptracer and ssh in pkg/profiles
1483 gforget 1.703 o profiles: adding ptracer and ssh
1484 jmc 1.702 o testreport: change multi-test output-file name
1485     (from output.txt.{name} to output.{name}.txt)
1486 jmc 1.712 o profiles: now ok for mutli-tiles case
1487 mlosch 1.700 o seaice: add 4 parameters for different advection schemes for area,
1488     (effective) seaice thickness, enthalphy, and snow height. Their default
1489     is the standard parameter SEAICEadvScheme
1490 jmc 1.699 o calc_gw:
1491     - add cosFacU in zonal viscous flux (harmonic.visc.).
1492     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
1493     of tutorial_plume_on_slope.
1494     o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1495 jmc 1.698 o calc_gw: true flux-form, account for horizontal grid spacing.
1496     update rotating_tank results, but not plume_on_slope (affected at
1497     truncation level, 11 digits).
1498    
1499 heimbach 1.697 checkpoint58l_post
1500 jmc 1.698 o calc_gw:
1501     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
1502     - remove side-drag for now (need to fix it); update plume_on_slope results.
1503     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
1504 heimbach 1.695 o commit code to make SST/SSS weights spatially variable
1505     (based on either variable in-situ or variable initial T/S weights)
1506 heimbach 1.696 o pkg/ecco:
1507     * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
1508     now based on horizontally varying weights wthetaLev, wsaltLev
1509     * cost_averagesflags now returns year indices in addition to day, month
1510     * sflux balance is performed on annual basis
1511     (sflxumm, sfluxmm2, bal_sfluxmm)
1512     * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
1513     including separate counting and multipliers
1514 heimbach 1.697 o pkg/rbcs
1515     * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
1516 jmc 1.694
1517 jmc 1.693 checkpoint58k_post
1518 jmc 1.692 o testreport:
1519     - always build in dir. "build" (if not there, mkdir build instead of building
1520     & running in input)
1521     - run in dir run (if it exists), in build otherwise.
1522     - call prepare_run (if input/prepare_run exists)
1523     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
1524 dimitri 1.691 o pkg/exf modifications to interpolation and rotation routines for more
1525     reasonable treatment of North Pole singularity: for tracers North Pole
1526     value is set to northernmost zonal-mean value, for zonal velocity it is
1527     set to zero, and for meridional velocity it is set to northernmost value.
1528 mlosch 1.690 o pkg/exf/exf_check_range.F
1529     - add tile index to diagnostics and move stop statement to the very
1530     end of the routine.
1531 jmc 1.689 o pkg/diagnostics: (diagnostics_main_init.F)
1532     define title of isomorphic variables according to the current config.
1533 jmc 1.687 o pkg/thsice with pkg/seaice dynamics:
1534 jmc 1.688 - fix domain of computation (interior only, required for exf) and do exchanges
1535     - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
1536 jmc 1.686 o towards a standard way of dealing with multi-threading in MONITOR
1537     and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
1538 baylor 1.685 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
1539     to W momentum equation in nonhydrostatic and quasihydrostatic runs.
1540 jmc 1.684 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
1541 jmc 1.683 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
1542     o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
1543     (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
1544 jmc 1.682 o tracer advection:
1545     - clean-up and simplify calc_common_factors.F
1546     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
1547     advection subroutine (but still not used within DST advection S/R)
1548 jmc 1.681 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
1549    
1550 heimbach 1.680 checkpoint58j_post
1551     o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
1552     from file (collects calls previously in FORWARD_STEP)
1553     o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
1554 heimbach 1.679 o adjoint store dir. adjusted accordingly
1555 heimbach 1.680 o genmake2
1556     replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
1557 heimbach 1.679
1558 jmc 1.678 checkpoint58i_post
1559 mlosch 1.677 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
1560     on wind stress (SEAICEstressFactor defaults to 1.)
1561 jmc 1.676 o Total number of Timers is finite (<=40): comment out 2 non-essential one
1562     in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
1563 jmc 1.675 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
1564     on CS-grid: no longer loosing mass.
1565 jmc 1.674 o exf & curvilinear-grid: no longer modify longitude xC & xG.
1566 mlosch 1.670 o pkg/ggl90: fix sloppy output and fix a bug
1567 dimitri 1.672 o pkg/seaice: added SEAICEuseEVPpickup parameter
1568     - Set to false in order to start EVP solver with
1569     non-EVP pickup files when using SEAICEuseEVP
1570 mlosch 1.673 - fix sign error in diffusion in seaice_calc_rhs
1571 mlosch 1.670
1572 heimbach 1.669 checkpoint58h_post
1573     * Modifications for bottom topography control
1574     o replace hFacC by _hFacC at various places
1575     o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
1576     o add non-self-adjoint cg2d_nsa
1577     o update autodiff support routines
1578     o re-initialise hfac after ctrl_depth_ini
1579     o works for 5x5 box, doesnt work for global_ocean.90x40x15
1580     * Adding verification for 5x5 box (4-layer) bottom topography control
1581    
1582 heimbach 1.668 checkpoint58g_post
1583 jmc 1.671 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
1584     used for mean seasonal cycle, mean diurnal cycle); add an example
1585     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
1586 mlosch 1.667 o pkg/ggl90:
1587     - add parameter (minimum surface kinetic energy)
1588     - fix bug (avoiding division by zero)
1589 mlosch 1.665 o couple pkg/thsice to pkg/seaice:
1590     - modify advection in seaice to accomodate new scalar fields to be advected
1591     - only muliDimAdection scheme work with seaice/thsice
1592     - mapping of thsice-variables to seaice-variables, back and forth
1593     - does not break the verification experiments, but does not give the
1594     desired results either
1595     o pkg/seaice
1596     - make (default) second order advection a bit less confusing?
1597    
1598 jmc 1.664 checkpoint58f_post
1599 mlosch 1.662 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
1600     to pkg/seaice):
1601     - new routines thsice_map_exf and thsice_get_exf provide the interface
1602     - add an additional formal parameter to thsice_solve4temp
1603 heimbach 1.661 o pkg/exf:
1604     - add new fields wspeed, snowprecip (to be able to couple to thsice)
1605     - correct Stefan-Boltzmann constant
1606     - new parameter for longwave surface emittance
1607     - separate some stuff from exf_bulkformulae into new routines
1608     exf_radiation, exf_wind
1609 mlosch 1.662 - add new parameters and constants: longwave emissivity for ocean, ice
1610     and snow, evaporation parameters over ice
1611 mlosch 1.663 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
1612     either wind from stress or stress from wind
1613 jmc 1.660 o pkg/thSIce:
1614     - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
1615     - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
1616     and THSICE_CALC_THICKN
1617     - for now, call to THSICE_GET_BULKF remains inside i,j loops.
1618     - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
1619     to make debugging easier.
1620     - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
1621     o pkg/bulk_force:
1622     - clean-up comments and parameters ;
1623     - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
1624 jmc 1.659 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
1625     generate new output for test-experiment: aim.5l_cs.thSI
1626 jmc 1.658 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
1627 heimbach 1.661 testreport accordingly
1628 jmc 1.658
1629 jmc 1.657 checkpoint58e_post
1630 heimbach 1.656 o SEAICE_CGRID adjoint done
1631 heimbach 1.654 o R_STAR adjoint implemented.
1632     * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
1633     * need to sort out init. of h0facc, etc.
1634 heimbach 1.655 o Make pkg/profile fully independent of ecco,cost, etc. stuff
1635     to be able to use it in pure forward.
1636 heimbach 1.653
1637 jmc 1.652 checkpoint58d_post
1638 jmc 1.651 o upgrade simple test-experiment to tutorial example:
1639     step.1: duplicate the experiment and (step.2) will remove the old copy.
1640     tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
1641     tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
1642     tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
1643     tutorial_global_oce_biogeo <- copy of dic_example
1644     tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
1645     tutorial_plume_on_slope <- copy of plume_on_slope
1646     tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
1647     tutorial_global_oce_optim <- empty for now (David ?)
1648     tutorial_global_oce_in_p <- copy of global_ocean_pressure
1649     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
1650 gforget 1.650 o correct a sign problem in cost_scat.F
1651 mlosch 1.649 o obcs and ptracers: fix boundary conditions for advections schemes
1652     with larger stencil
1653 heimbach 1.648 o thsice adjoint: start
1654 mlosch 1.647 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
1655     completeness
1656 mlosch 1.646 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
1657     and COSINEMETH_III, add comments in default CPP_OPTIONS.h
1658 heimbach 1.645 o ptracers adjoint:
1659     * avoid extensive recomputatations
1660     * fix missing re-init. of gptr (missed by TAF)
1661 mlosch 1.644 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
1662     me to turn off the excessive output to STDOUT that this package produces
1663 jmc 1.643 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
1664     and add those terms in Vector-Invariant formulation.
1665 gforget 1.642 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
1666     if the control period (xx_hfluxperiod etc) is 0
1667     o in profiles pkg, clean routines and fix details
1668     o in ecco pkg, reading ssh data:
1669     fix problem in case the model does not start at iter0=0
1670 mlosch 1.640 o fix mnc-pickup/restart for ptracers
1671 heimbach 1.641 o new package prifiles:
1672     code to compute profile-based cost by Gael Forget
1673 heimbach 1.639 (modifs in ecco, ctrl, autodiff)
1674 heimbach 1.641 o Benign bug fix in initialization (spotted by M. Mazloff) of
1675     ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
1676 heimbach 1.639
1677 heimbach 1.638 checkpoint58c_post
1678     o adjoint: finish NLFS adjoint and provide reference output in
1679     verification/global_ocean.90x40x15/results_ad_nlfs
1680 mlosch 1.637 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
1681     documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
1682     SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
1683     with SEAICE_CGRID defined.
1684 jmc 1.636 o move calendarDumps from "data" to "data.cal" and clean-up the code
1685     with a simple call to pkg/cal S/R: CAL_TIME2WRITE
1686     o add useEXF & useCAL flags (for now, set in hard-coded way)
1687 jmc 1.635 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
1688     (were missing in NH mode, and wrong in quasihydrostatic mode).
1689     waiting for Chris updated version of calc_gw to add those CALLs.
1690     o fix bug in quasihydrostatic S/R ;
1691     add a test for this option: global_ocean.90x40x15.qshyd
1692 jmc 1.634 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
1693     (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
1694     o add on/off flag useOffLine for package OFFLINE
1695 mlosch 1.630 o seaice:
1696     - modify advection so that it works also on the C-grid
1697     - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
1698     problem in multi-tile runs with C-grid
1699 mlosch 1.633 - add flags for clipping ice velocities and/or masking solver forcing
1700 mlosch 1.631 - fix drag (ocean on ice) formulation and a bug that caused noise in the
1701     C-grid solver
1702 mlosch 1.632 - added a few comments to seaice_diffusion.F
1703     - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
1704     are now exclusive)
1705     - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
1706     required re-ordering the code a little:
1707     + make DAIRN global variable (defined in SEAICE)
1708     + move computation of the viscosities eta and zeta into a new separate
1709     routine (because I need to recompute them in seaice_ocean_stress.F)
1710 mlosch 1.629
1711 jmc 1.628 checkpoint58b_post
1712 jmc 1.627 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
1713     update output.txt of exp. aim.5l_cs.thSI
1714 edhill 1.626 o various mnc cleanups and improvements:
1715     + shrink lookup tables by factor of ~4
1716     + better error reporting when running out of lookup space
1717     + able to handle longer path/file names (up to 500 chars)
1718 heimbach 1.625 o adjoint:
1719     - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
1720     - TBD: "hidden" mom_vecinv recomp. in dynamics
1721 jmc 1.624 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
1722     (allow to differentiate between forcing components using new integer flags:
1723     momForcingOutAB=1/0 & tracForcingOutAB=1/0)
1724     and add new flag to put Dissipation tendency out of Adams-Bashforth.
1725 heimbach 1.623 o ecco
1726     - enable trend removal from SSH anomaly obs.
1727     o adjoint
1728     - a fix for PmEpR when #undef EXACT_CONSERV
1729     - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
1730     - try to fix "hidden" recomp. in forward_step for NLFS
1731     (NLFS seems broken sometimes after I checked it in)
1732 mlosch 1.622 o seaice:
1733     - add c-grid version of the dynamic solver:
1734     + three new routines that are the c-grid substitute lsr, dynsolver
1735     and ostres
1736     + put a few fields that were local to dynsolver into global common
1737     blocks, so that I can move the computation of stresses etc into
1738     seaice_lsr (saves coding but may break the adjoint).
1739     - replace more hardwired parameters by runtime parameters
1740     - add ice masks that mask the rhs of the implicit solvers where there
1741     is no ice (commented out in seaice_dynsolver, because i am not sure
1742     if this works properly), eventually this should replace the clipping
1743     of ice velocities in seaice_dynsolver to +/-40cm/s.
1744 edhill 1.621 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
1745     include it only where its needed
1746 mlosch 1.620 o move balancing of fluxes before the call of external_forcing_surf
1747 mlosch 1.619 o seaice:
1748     - correct units of turning angles (now they are really in degrees)
1749     - move computation of GWATX/Y out of main routine into dynsolver
1750     - initialize GWATX/Y in seaice_init
1751 jmc 1.618 o Apply mask on Fresh-Water flux (needed for SSH forcing).
1752 mlosch 1.619 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
1753 mlosch 1.617 o seaice: add runtime flags for turning angles (default to zero)
1754 heimbach 1.616 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
1755     and trend from exf forcing and ctrl control adjustments
1756     o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
1757     (since checkpoint57x_post)
1758 jmc 1.615 o change the default rotation period to 86164.s = the Earth rotation
1759 jmc 1.614 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
1760     and based on a reference stratification. Tested within hs94.cs-32x32x5.
1761 mlosch 1.613 o seaice advection: add code for choosing between the default (2nd order
1762     central differences) and multiDim advection schemes provided by
1763     pkg/generic_advdiff
1764 mlosch 1.611 o seaice:
1765     - removed all references to SEAICE_GRID.h fields from
1766     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
1767     (cubed-sphere configuration will change a little)
1768     - grid computations in seaice_init are obsolete now.
1769     - cleaned up code a little so that is easier to read (hopefully).
1770 mlosch 1.613 - added new (better?) discretizations of default advection and diffusion
1771     (turn on with SEAICEuseFluxForm)
1772     - replace 1 in 3d global fields by kSurface in growth.F
1773 mlosch 1.611
1774 mlosch 1.610 checkpoint58a_post
1775 mlosch 1.612 o seaice:
1776     - bug fix in advect.F
1777 mlosch 1.608 o shelfice:
1778     - separate shelfice load anomaly from pload (breaks with time
1779     dependent forcing), => introduce constant field shelficeLoadAnomaly.
1780     Its default is 0., but it may be computed more cleverly from (unknown)
1781     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
1782     done offline. A good approximation of the pressure load anomaly is
1783     necessary to avoid large initial adjustment processes underneath
1784     deep-reaching shelfice.
1785 mlosch 1.609 - small fix in ISOMIP shelfice_thermodynamics
1786     - add more sophisticated thermodynamics of Hellmer (1989), this is
1787     now the default
1788     - give a few constants more intuitive names
1789 mlosch 1.607 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
1790     if bulk formulae are used in long integration (especially EmPmR). Turn
1791     on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
1792     if balancePrintMean, the imbalance that is substracted is printed to
1793     STDOUT.
1794 jmc 1.606 o fix bug (typo) in obcs_apply_eta.F
1795 mlosch 1.605 o add a new package shelfice which enables us to model the circulation
1796     underneath shelf-ice with draughts of hundreds of meters.
1797     - works
1798     - to do: + include improved thermodynamics
1799     + check whether kSurfC (from model/inc/SURFACE.h) can be used
1800     instead of new field kTopC
1801     + can we use topoFile, Ro_surf and existing code in ini_depth.F
1802     instead of new field R_shelfIce and new code in ini_depth.F
1803     and ini_mask_etc.F?
1804 mlosch 1.608 + adjust vertical mixing schemes?
1805 mlosch 1.604 o seaice pkg:
1806     - add a cpp-flag to include a simple formula for a salinity dependent
1807     freezing point of sea water at the surface
1808     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
1809     meridional stresses are now different (and hopefully correct)
1810 jmc 1.602 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
1811     update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
1812     and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
1813 jmc 1.601 o pkg/diagnostics: add options and parameters for regional-statistics
1814     diagnostics ; define regions by reading a region-mask from a file
1815     (might add other options later)
1816 jmc 1.600 o pkg/bulk_force:
1817     - add option and parameters to use AIM surface-flux formulae.
1818     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
1819     others forcing fields (defined in PARM05, parameter file "data") are loaded
1820     from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
1821     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
1822     - use the right EXCH call for uwind,vwind (to work on CS-grid).
1823     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
1824     and parameters (note: calcWindStress replaces .NOT.readwindstress).
1825     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
1826    
1827 jmc 1.599 checkpoint58
1828 edhill 1.598 o add "--embed-source" option to genmake2 which, when the supporting
1829     tools can be compiled (as determined by genmake2) will turn on the
1830     embed_files package which then embeds the entire MITgcm source code
1831     (*.[fFhc] + Makefile) used for the build within the executable
1832     - requested by CNH but off by default
1833     - adds a paltry <9MB to the mitgcmuv executable in most cases
1834     - only writes the output when useEMBEDSRC in eedata is true
1835 heimbach 1.597 o clean up 3-dim. relaxation codes:
1836     * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
1837     * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
1838     * Thanks to Tom Haine for testing!
1839    
1840 jmc 1.596 checkpoint57z_post
1841 jmc 1.593 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
1842     affects output (@ truncation level) of exp. plume_on_slope ; updated.
1843 mlosch 1.592 o fix the pickup behavior for obcs in combination with ptracers
1844     o fix a bug in ptracers_external_fields_load
1845     o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
1846     affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
1847     o transfered surface NH pressure to eta field (if exactConserv).
1848 jmc 1.589 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
1849     and update lab_sea output.txt file.
1850 heimbach 1.590 o completing 3-dim. relaxation code: additional term
1851     1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
1852     in S/R EXTERNAL_FORCING_T (file external_forcing.F)
1853     * At compile time, in "EXF_OPTIONS.h" set
1854     #define ALLOW_CLIMTEMP_RELAXATION
1855     #define ALLOW_CLIMSALT_RELAXATION
1856     * At runtime in "data", under &PARM03 set (e.g., units in seconds)
1857     tauThetaClimRelax3Dim = 15552000.0,
1858     tauSaltClimRelax3Dim = 15552000.0,
1859     * 3 cases:
1860     1) Use a constant-in-time 3-dim. field
1861     2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
1862     3) Real-time relax. to time-evolving prescribed field
1863 heimbach 1.595 o Adding Laplacian-type smoothness constraint on
1864     initial and boundary (forcing) controls (ic, bc)
1865     * enable at compile-time via
1866     ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
1867     * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1868 heimbach 1.594 * Absolute scale somewhat unclear so far
1869     * no area weighting was included since no other cost term does so far
1870 jmc 1.589
1871 heimbach 1.588 checkpoint57y_post
1872     First step for a NLFS adjoint
1873     o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
1874     o new init. routines for calc_r_star, calc_surf_dr
1875     o still need to deal with ini_masks_etc
1876     o testreport seemed happy
1877 heimbach 1.587 checkpoint57y_pre
1878    
1879 jmc 1.586 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1880 stephd 1.585 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1881 stephd 1.584 o add new offset feature to offline pkg (plus minor cleanup)
1882     o cfc fixes for final year of integration
1883     o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1884     be in GCHEM_OPTIONS).
1885    
1886 jmc 1.583 checkpoint57x_post
1887     o fix testreport Pb in multiple test experiment.
1888 edhill 1.582 o cleanup our namelist syntax in verification:
1889     - make it more F95 standards compliant (some work still needed)
1890     - allows the vast majority of our tests to work with gfortran
1891 jmc 1.580 o Non-Hydrostatic:
1892     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1893     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1894 jmc 1.579 o Allow to apply AB on T,S rather than on AB(gT,gS):
1895     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1896     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1897     time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1898     - need a "clever" read_pickup to restart from the other AB formulation
1899 jmc 1.578 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1900     o remove some unused variables (reduces number of compiler warnings)
1901 heimbach 1.581 o adjoint
1902     * Disable useVariableViscosity for adjoint for time being
1903     (there are a number of extensive recomputations)
1904     * Initialize certain variables needed for adjoint
1905 jmc 1.578
1906 jmc 1.577 checkpoint57w_post
1907 jmc 1.576 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1908     fix the singleCpuIO RS version of MDSWRITEFIELD
1909     and add a WARNING if using globalFiles=T with multi-processors.
1910 jmc 1.575 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1911     using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1912 jmc 1.576 o tracer advection scheme:
1913 jmc 1.574 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1914     those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1915     was not very convenient).
1916     add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
1917     (further tests needed for the implicit DST & Flux-Limiter schemes).
1918 mlosch 1.573 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1919     and sRef for convenience, handy, when you want to initialize
1920     ptracers in a large domain with a constant non-zero value. Also,
1921     untangle ptracers_init.F a little.
1922    
1923 jmc 1.572 checkpoint57v_post
1924     o change dome exp. to use variable viscosity in side-drag terms.
1925 edhill 1.570 o remove all the files from the cfc_offline test since they are now
1926     incorporated into tutorial_cfc_offline which has been producing
1927     identical results for a few days of testing
1928 jmc 1.571 o add new parameter: sideDragFactor to enable half-slip-side BC
1929     and change side-drag S/R to use viscosity from mom_calc_visc
1930     (can switch back by setting sideDragFactor=0.); affects results at
1931     truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1932     global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1933 jmc 1.569 o vorticity & strain are now computed without masking, to account for
1934     no-slip-side BC in variable viscosity calculation ; mask is applied
1935     anyway later on, before computing advection/coriolis terms.
1936 mlosch 1.573 o modify exp4 to test new obcs support for reading from external files
1937 mlosch 1.568 and for passive tracers
1938 mlosch 1.567 o fix behavior of ptracers_monitor when monitor output is written to a
1939     netcdf-file; still not independent of monitor.F (writes in the same
1940     file).
1941 jmc 1.566 o change default value of tRef (put a uniform, meaningful value for ocean
1942     & atmos) and initialize sRef (was missing, as Martin mentioned).
1943 baylor 1.565 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
1944     to be proportional to enstrophy dissipation length. Thus,
1945     viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1946     This is now consistent with Smagorinsky and with the manual.
1947    
1948 mlosch 1.564 checkpoint57u_post
1949 mlosch 1.562 o OBCS and PTRACERS: add open boundary support for passive tracers
1950     - either use homogenous (pseudo) v.Neumann conditions or prescribe
1951     OB-values from file; this is not different from the way theta and salinity
1952     are treated
1953     - however, Orlanski-radiation conditions are not supported, and the model
1954     will stop if you use pTracers and Orlanski at the same time.
1955     - beefed up the rountine obcs_external_fields_load: now only those open
1956     boundary values are overwritten with values from files for which there
1957     are really files, otherwise the OB-fields remain untouched. This makes
1958     it possible to use different OBs at different ends of the domain (as
1959     with EXF)
1960 jmc 1.561 o reduce number of exch calls in shap_filt (s2).
1961 jmc 1.560 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1962     truncation level) 4/5 MLAdjust test results (11&12 digits match).
1963    
1964 jmc 1.559 checkpoint57t_post
1965 jmc 1.558 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1966     o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1967     same truncation, independent of the face number: affects affects several
1968     test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1969 jmc 1.557 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1970 jmc 1.558 note that biharmonic viscosity + no-slip was not tested in any experiment.
1971 jmc 1.556 o fix bug in non-linear free-surf side-drag ; generate new output for
1972     global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1973 edhill 1.555 o make mnc honor the writeBinaryPrec flag for most kinds of output
1974 edhill 1.554 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1975 jmc 1.553 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1976     error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1977 jmc 1.552 o add brackets in multi-terms sum to get same truncation, independent of
1978     the face number (manage to get exactly same value of gU,gV at the cs-edge)
1979     affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1980 baylor 1.551 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
1981     and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1982     a maximum grid-scale Reynolds number. Also, changes all length calculations
1983     in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1984     Suggested values of viscosity parameters found in mom_calc_visc.
1985     Many new viscosity diagnostics available.
1986 jmc 1.550
1987     checkpoint57s_post
1988 baylor 1.549 o Add clearing-house for viscosity calculations, mom_calc_visc and
1989     correct numerous bugs in LeithD and Smagorinsky discretizations.
1990     mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1991     used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1992     Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1993     and with Strain-Tension viscous term calculation (mom_hdissip.F).
1994     The Strain-Tension form is now called with useStrainTensonVisc=.true.
1995     ViscAhStrain and viscAhTension are now retired.
1996 jmc 1.550 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1997 edhill 1.547 o In response to JMC's bug report, genmake2 now ignores any soft-links
1998     that it finds in the *current* directory when searching for files.
1999     Soft-links found in any other source directories will still work as
2000     they did before.
2001 edhill 1.546 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
2002     a C routine to unlimit the stack size
2003 edhill 1.545 o mnc-ify pkg/aim snapshot vars
2004 edhill 1.544 o mnc-ify pkg/land as requested by Daniel
2005 edhill 1.543 o various changes to mnc including:
2006     - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
2007     - output can now be grouped so that all files within a group
2008     change the ITER portion of their names in lock-step together
2009     - can now read ("global") PER-FACE (in addition to PER-TILE) files
2010     and works with both EXCH1 and EXCH2 (but needs more testing)
2011     - writing works for all verification test cases w/ g77 on Linux
2012    
2013 jmc 1.542 checkpoint57r_post
2014 edhill 1.541 o make MNC variable initialization happen earlier
2015 jmc 1.540 o add diagnostics for (almost) each term of the momentum Eq.
2016 jmc 1.537 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
2017 jmc 1.536 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
2018     o remove MINIMAL_TAVE_OUTPUT option ;
2019     add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
2020 jmc 1.535 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
2021     allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
2022 heimbach 1.538 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
2023     o add time-dependent SST, SSS control
2024 heimbach 1.539 o cost terms in ecco/ modularized (new cost_generic.F)
2025     o cost_averages routines are modularized (new cost_averagesgeneric.F)
2026     o new infrastructure for seaice model vs. obs misfits in seaice/
2027     * driver from the_main_loop.F is seaice_cost_driver.F
2028     * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
2029     * gradient check in Exp. 6a of natl_box_adjoint/
2030     o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
2031     (see README file)
2032 jmc 1.535
2033 heimbach 1.534 checkpoint57q_post
2034 jmc 1.533 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
2035 edhill 1.531 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
2036     - bug was reported by Jean-Michel and Ian Fenty
2037 jmc 1.532 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
2038     update exp. cpl_aim+ocn output.
2039 heimbach 1.530 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
2040     Needed for high-res. runs with large global files
2041     to be able to limit tapelev size
2042     o Changed some tests for adjoint:
2043     * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
2044     * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
2045     * global_ocean.90x40x15/ back to default 3-level checkpointing
2046 heimbach 1.534 o Modifications to enable scripted COMMON to MODULE conversion
2047     * verification/OpenAD/code/ has necessary scripts and description;
2048     * converts, compiles and runs successfully;
2049 heimbach 1.530
2050 jmc 1.529 checkpoint57p_post
2051     o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
2052     o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
2053     (already the case for some pkgs, including recent MNC_init, e.g. thsice)
2054     o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
2055 jmc 1.527 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
2056     (was already the case for dissipation with mom_vecinv,
2057     and also the case for grad.PhiHyd when staggered-timeStep)
2058     This will allow to put dissipation out-off the AB time-stepping.
2059     Unfortunately, affects truncation error. Update output of exp. that "fails"
2060     (cg2d matching number) and leave the others for later: front_relax(10),
2061     global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
2062     matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
2063    
2064 heimbach 1.526 checkpoint57o_post
2065 edhill 1.525 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
2066     (2) its ready to be documented during the 20050801 DocFest
2067 edhill 1.524 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
2068     for ideal_2D_oce and lab_sea on linux_ia32_g77
2069 heimbach 1.526 o set to #undef CTRL_SET_OLD_MAXCVARS_30
2070     in global1x1_tot/code_seaice_adj to access indices 32, 33
2071     (worth another tag)
2072 edhill 1.524
2073 heimbach 1.523 checkpoint57n_post
2074 heimbach 1.521 o adding precip control xx_precip 32
2075     o adding swflux control xx_swflux 33
2076 heimbach 1.522 o Replacing 10 forcing penalty cost routines by 1 generic.
2077     o Implementing partitioning in time-mean and variable adjustment
2078     for atmos. state.
2079     o Time-mean constant error is now read in data.ecco (instead of hard-coded)
2080 heimbach 1.519 o in natl_box_adjoint:
2081 heimbach 1.522 * updated exp 1 to 10
2082     (but does not have time-mean vs. variable split results yet)
2083 heimbach 1.523 o updated global1x1/*_seaice_adj/
2084     to incorporate latest changes
2085 heimbach 1.520 o enable useSingleCpuIO for mdsio vector routines
2086     (applies in particular to tapelev I/O)
2087     o removed inefficient K-loop in all active_file*control*.F
2088 heimbach 1.518
2089 heimbach 1.517 checkpoint57m_post
2090 jmc 1.516 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
2091     and advect_cs (use EXCH-2 and standard cs-32 grid files).
2092 jmc 1.515 o pkg/exch2: filling of face-corner halo regions is optional
2093     (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
2094    
2095 jmc 1.514 checkpoint57l_post
2096     tag before updating tutorials (pre-release-2)
2097 jmc 1.513 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
2098     for output and interpolation of input fields onto model grid)
2099     o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
2100     Affects results of exp. rotating_tank ; update output.txt.
2101 jmc 1.511 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
2102 jmc 1.512 and taking the square quantity and/or using a fraction-weight field.
2103 jmc 1.511 o fix aim_diagnostics_init.F mate numbers.
2104     o add mnc output capability to diagnostics/diagstat and update
2105 edhill 1.510 our cvsignore files for the ACSII output generated
2106    
2107 heimbach 1.509 checkpoint57k_post
2108     o lab_sea now uses diagnostics package and provides a suite of
2109     new EXF diagnostics output.
2110    
2111 heimbach 1.508 checkpoint57j_post
2112     o exf
2113     * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
2114     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
2115     terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
2116     * extended diagnostics output
2117     - now includes all EXF variables
2118     - hs, hl moved to common block
2119     - separate S/R for diagnostics, called after ctrl vector is added
2120     - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
2121     - EXFqnet contains true Qnet (i.e. includes qsw)
2122     * updated verif. lab_sea, global_with_exf
2123     * Rearranging hflux (exf_mapfields -> exf_getforcing)
2124     to ensure that diagnostics sees a true EXFqnet
2125 jmc 1.507 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
2126 jmc 1.506 o diagnostics pkg: change pointers so that 1 diagnostic can be used
2127     several times with different frequencies.
2128 edhill 1.505 o mnc-ify the thsice package as requested by Daniel Enderton
2129     - the monitor--MNC output needs work
2130     - many attributes need to be added (most are currently blank)
2131     o mnc-ify theaim_v23 package as requested by Daniel Enderton
2132     - many attributes need to be added (most are currently blank)
2133 jmc 1.503 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
2134 jmc 1.502 o add Sadourny like discretization to the 4th.O vorticity advection scheme
2135 jmc 1.500 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
2136 jmc 1.501 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
2137     fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
2138 jmc 1.499 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
2139     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
2140    
2141 jmc 1.498 checkpoint57i_post
2142 molod 1.497 o Diagnostics package was changed: diagnostic allocation is now deactivated
2143     by setting an empty file name in the namelist (used to be by setting 0 frequency)
2144 jmc 1.496 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
2145     add 1rst Order upwind vertical Shear.
2146 edhill 1.495 o add a quick fix for A/B checkpointing in OFFLINE mode
2147 edhill 1.494 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
2148     end-run around the C/Fortran linking horror in eesup/src/timers.F
2149 adcroft 1.493 o added pkg/runclock: allows user to terminate run based on wall clock
2150     o added non-hydrostatic scaling parameter: nh_am2
2151 mlosch 1.492 o pkg/my82: futile attempt to make results compiler-independent by adding
2152     some "_d 0", etc. no effect.
2153 edhill 1.491 o for mnc output, fill the 'T' coordinate var with myTime and create a
2154     separate 'iter' variable for iteration count
2155 jmc 1.489 o pkg/diagnostics:
2156 jmc 1.490 add new capability: output of Global/Regional & per-level statistics ;
2157     tested against monitor output (including land & thSIce) on various exp.
2158     o make seaice-pkg I/O type flags (MNC/MDS) more standard.
2159 jmc 1.489
2160 jmc 1.488 checkpoint57h_done
2161     tag after changing user customized files (DIAGNOSTICS_SIZE.h,
2162     data.diagnostics, data.gchem, data.ptracers) is done.
2163    
2164 jmc 1.487 o pkg/diagnostics: prepare for Global/Regional statistics.
2165     add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
2166 jmc 1.486 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
2167     and rename it: DIFFERENT_MULTIPLE
2168    
2169 jmc 1.485 checkpoint57h_post
2170     o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
2171 jmc 1.484 o pkg/diagnostics: change output frequency, now in seconds (instead
2172     of Nb of iterations). This requires to change data.diagnostics.
2173 jmc 1.483 checkpoint57h_pre
2174    
2175 edhill 1.482 o in mnc, let the user create the output dir if both mnc_outdir_date
2176     and mnc_outdir_num are false
2177 edhill 1.481 o add fflags() to pkg/diagnostics which allows one to specify, on a
2178     per-file basis, the file precision [default behavior is unchanged]
2179 dimitri 1.480 o added diagnostics to pkg/kpp, including computation of mixed layer
2180     depth based on a temperature/density criterion
2181     o updated verification/natl_box to test the new pkg/kpp diagnostics
2182 jmc 1.479 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
2183 jmc 1.478 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
2184 edhill 1.477 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
2185     not mnc -- this mistake was found by JMC and is now corrected
2186    
2187 jmc 1.476 checkpoint57g_post
2188     o add Adams-Bashforth 3rd Order time stepping:
2189     - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
2190     - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
2191 jmc 1.475 checkpoint57g_pre
2192    
2193 heimbach 1.472 o make lambda[Theta,Salt]ClimRelax spatially varying
2194     (default remains spatially uniform constant based on tau)
2195 heimbach 1.473 o added new control variables
2196     * init. uVel, vVel, etanN
2197     * lambda[Theta,Salt]ClimRelax
2198     o separate masks used for ctrl_pack/unpack 'from write_grid' output
2199     (suggested by G. Forget)
2200 heimbach 1.472
2201 jmc 1.471 checkpoint57f_post
2202     o add parameter "baseTime" = model base time = time at iteration zero
2203     new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
2204     account for baseTime shift
2205     o move Coriolis arrays from PARAMS.h to GRID.h
2206 jmc 1.470 checkpoint57f_pre
2207    
2208 edhill 1.468 o mnc-ifying the seaice package
2209 adcroft 1.467 o introduced an alternative length scale calculation for use in the limiting
2210     maximum viscosity (off by default, see mom_vi_hdissip.F for details)
2211 heimbach 1.466 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
2212 baylor 1.465 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
2213     as well as grad(vort3). Made it compatible with both approximate form
2214     for the cubed sphere and full form of these gradients. Added flag
2215     useFullLeith to select between approximate and full form.
2216 jmc 1.464 o add "d0" in getcon.F to reduce differences between compilers/platforms
2217     update output.txt of exp. fizhi-gridalt-hs
2218 jmc 1.463 o change port_rand funtion to allow to set the seed.
2219 edhill 1.462 o fix obscure MNC bug involving conversion between reals and integers
2220     - it caused no problems with certain (eg. gcc, ifc) compilers but the
2221     new version is now more standards-compliant
2222 heimbach 1.469 o adjoint-related modifications
2223     * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
2224     * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
2225     * mom_vi_hdissip: to be able to use Leith scheme in adjoint
2226 edhill 1.462
2227 heimbach 1.461 checkpoint57e_post
2228     o Adding eddy stress controls a la Ferreira et al.
2229 jmc 1.474 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
2230 heimbach 1.460
2231 jmc 1.459 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
2232     update output.txt of exp. fizhi-gridalt-hs
2233 edhill 1.458 o add more "Z" dimensions and associated coordinate vars to MNC
2234 dimitri 1.457 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
2235 dimitri 1.456 o parameter calendarDumps: when set, approximate months (30-31 days) and years
2236     (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
2237     KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
2238     months and years. Requires pkg/cal.
2239 edhill 1.455 o diagnostics: add pickup functionality
2240     - off by default for backwards compatibility
2241     - current version only uses MDSIO -- MNC will be added
2242 jmc 1.454 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
2243 jmc 1.452 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
2244    
2245 jmc 1.451 checkpoint57d_post
2246     o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
2247 edhill 1.450 o modify verification/ideal_2D_oce so that it tests the creation of mnc
2248     output from the diagnostics package
2249 jmc 1.449 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
2250 edhill 1.448 o make genmake2 more portable by using ".$FS" instead of ".f" for more
2251     of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
2252 edhill 1.447 o add coordinate variables to the MNC output from the diagnostics package
2253 jmc 1.446 o change MNC-flags default value: true when useMNC=TRUE
2254 edhill 1.444 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
2255     the ability (off by default) to read the grid information using MNC
2256 jmc 1.445 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
2257 jmc 1.443 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
2258 jmc 1.442 o do snap-shot diagnostics at the middle of the time-interval (instead of
2259     at the end).
2260 jmc 1.441 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
2261     new test for AIM with thSIce + slab-ocean
2262 jmc 1.440 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
2263 jmc 1.439 o move state variable diagnostics to the beginning of the time step ;
2264     (note: still needs some work specially for snap-shot diagnostics)
2265     duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
2266    
2267 jmc 1.438 checkpoint57c_post
2268     o Change testing option (-ieee) to get closer agreement between g77 & ifort
2269     o generate new output.txt files on faulks with g77 & the new -ieee option
2270 jmc 1.437 checkpoint57c_pre
2271    
2272     o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
2273 jmc 1.436 update output.txt of exp. global_ocean.90x40x15
2274 jmc 1.435 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
2275     results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
2276 jmc 1.432 o add saltFlux(+File) forcing capability with periodicExternalForcing
2277 jmc 1.431 o allow to use pkg diagnostics for GM-Redi & ThSIce output
2278     o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
2279 edhill 1.430 o improvements for the MNC output from DIAGNOSTICS:
2280     - correct handling of the unlimitied dimension
2281     - all dims now have associated coordinate variables
2282     - variables located at U, V, and Corner ("Z") points are now written
2283     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
2284     *all* data points are output
2285 dimitri 1.429 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
2286 dimitri 1.428 o added pkg/seaice/seaice_monitor.F
2287 dimitri 1.427 o mdsio_readfield.F can now read files visible only to master MPI process.
2288 dimitri 1.426 o pkg/seaice: some test code for ice-modified ocean stress
2289 dimitri 1.425 o exf_getffields interpolation defaults to bilinear for all scalar forcing
2290     fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
2291     spurious negative numbers for precipitation and humidity. Will cause
2292     some small numerical differences for integrations using pkg/exf/exf_interp.F.
2293 heimbach 1.434 o pkg/ctrl/
2294     * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
2295     May be enabled via doPackDiag
2296     * introduce z-scaling of
2297     + gradient (doZscalePack) and
2298     + control (doZscaleUnpack)
2299     o pkg/mdsio/
2300     * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
2301     * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
2302 dimitri 1.425
2303 jmc 1.424 checkpoint57b_post
2304     o simplify options in diagnostics_fill arguments (remove weird combinations)
2305 edhill 1.423 o fix MNC coordinate variables so that they now contain per-face index
2306     values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
2307     general, EXCH2 grids are only aligned to a "local" coordinate system
2308 jmc 1.422 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
2309     o Implement instantaneous output within pkg diagnostics:
2310     setting a negative frequency in data.diagnostics produces
2311     "snap-shot" output (as opposed to time-average if freq > 0)
2312 jmc 1.421 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
2313     NOTE: change ptracer diagnostics name: use 2 characters to work with
2314     more than 9 tracers. Add also diagnostics of advect & diffus flux.
2315 edhill 1.420 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
2316     becomes the coordinate variable for the 'T' dimension
2317 edhill 1.419 o add CF-style coordinate variables to MNC
2318     - just a first cut: numbers are meaningless on the cubesphere and
2319     missing along the T axis but otherwise it works!
2320 dimitri 1.418 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
2321 jmc 1.417 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
2322 jmc 1.416 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
2323     this is based directly on what the model compute, so that the content of
2324     each diagnostics might be affected by switching options (e.g., implicitDiffusion)
2325     o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
2326 mlosch 1.415 o clean up build options files for SunOS, in particular
2327     - remove -traditional from xmakedepend
2328     - change -xarch=v9 to -xarch=native for f77
2329     - restore use of make (not gmake)
2330     - add CC=gcc if using g77
2331 edhill 1.413 o changes per discussion of AM, JMC, & EH3 today:
2332     - move redundant "grid" variables out of "state" -- in preparation of
2333     creating proper CF-style coordinate variables and in recognition
2334     that any/all grid variables can be easily copied (eg. w/NCO) from
2335     the grid files into any of the other NetCDF files
2336     - *always* output grid variables with MDSIO (this will eventually be
2337     changed)
2338     - output MNC grid file if useMNC is true
2339 edhill 1.412 o every instance of _END_MASTER() has been found and replaced with
2340     _END_MASTER( myThid ) in order to satisfy certain picky Sun
2341     preprocessors
2342 jmc 1.411 o re-arrange diagnostics pkg initialisation:
2343     - allow each package to extend the available diagnostics list
2344     - add some checking and fix small problems (multi-threaded, ...)
2345     - new S/R diagnostics_fill (replace fill_diagnostics):
2346     look through the short list of active diag. (instead of the long list)
2347     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
2348 edhill 1.381
2349 heimbach 1.410 checkpoint57a_post
2350     o this set of changes restores TAMC compatibility
2351     tested for global_ocean.90x40x15 adjoint on trough
2352     (what a pain)
2353    
2354 heimbach 1.409 checkpoint57a_pre
2355     o some modifs in tools/build_options for sunos
2356     o call ctrl_pack for ctrl at end for optimcycle=0
2357    
2358 jmc 1.408 checkpoint57
2359 mlosch 1.406 o add horizontal bi-harmonic viscosity for vertical velocity
2360     - new parameter viscA4W (defaults to viscA4)
2361     - affects only non-hydrostatic code
2362     - to be done: no-slip lateral boundary conditions
2363 dimitri 1.405 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
2364 jmc 1.404 o implement Implicit Vertical advection for pTracers
2365 jmc 1.401 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
2366 jmc 1.402 (implemented also for implicit vertical diffusion & advection)
2367 mlosch 1.400 o OBCS: extend application of tracer open boundary conditions
2368     to a strip beyond the boundary of width Olx/Oly
2369 heimbach 1.403 o add call monitor to TAF set of required calls (flow directives)
2370     and include in natl_box_adjoint
2371     o untangle a few ifdefs related to cost, ctrl, autodiff
2372     untangel a few ALLOW_ECCO_OPTIMIZATION
2373 heimbach 1.407 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
2374     (theta2, salt2 in ecco_cost_weights)
2375 mlosch 1.400
2376 mlosch 1.399 checkpoint56c_post
2377     o OBCS as control variables
2378     - update ctrl_ad_diff.list, obcs_ad_diff.list
2379     - remove balance of obcs controls from default
2380     - fix index bug nobcs in ctrl_init
2381     - fix dummy fields filen in ctrl_pack
2382     - add dummy weights for obcs
2383     o lsopt: comment out fort.94 output
2384     o optim:
2385     - remove unnecessary header files
2386     - adjusted namelists
2387     - add xerbla.F to Makefile
2388     o exf:
2389     - multiple modifications of exf_check_range
2390     - unit change in exf_init_runoff from [m/year] to [m/s]
2391     o mdsio:
2392     - i/o-vector change debugLevel from debLevA to debLevB
2393    
2394 mlosch 1.398 checkpoint56b_post
2395 mlosch 1.397 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
2396     is called from DO_THE_MODEL_IO
2397     - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
2398     - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
2399     - clean up PTRACERS_WRITE_TIMEAVE a little
2400 mlosch 1.396 o add another verification experiment that tests both the cfc-pkg and
2401     the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
2402     reactive tendencies treated inline with regular timestepping
2403 mlosch 1.395 o testreport previously did a lousy job of comparing small numbers, so
2404     we (Ed and Martin) changed the way the cut-off of 1.e-12 is
2405     implemented in the little c-progam tmp_cmpnum.c which is embedded in
2406     testreport.
2407     o ptracers_monitor: bug fix for MPI
2408    
2409 mlosch 1.394 checkpoint56a_post
2410     o GCHEM: finish reorganizating the package
2411     - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
2412     (introduces another 3D-array for each passive tracer, but only if
2413     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
2414     gchemTendency is not needed because the timestep is done separately)
2415     - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
2416     - GCHEM is now---more or less cleanly---separate from PTRACERS
2417     - to bo done: handling of surfaceForcingPtr that is needed for KPP not
2418     so clear to me how that should be done in a general way.
2419     o CFC: improve formatting of output in CFC_ATMOS
2420     o PTRACERS:
2421     - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
2422     that ALL experiments with ptracers enable can be checked. This makes
2423     GCHEM_MONITOR obsolete.
2424     - include a runtime parameter PTRACERS_monitorFreq that defaults to
2425     monitorFreq
2426     - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
2427 edhill 1.393 o add PTRACERS (PTR0[1-5]) to testreport output
2428 heimbach 1.391 o exf_check_range:
2429     * default changed to .TRUE.
2430     * will check values for niter0 if debLevA, every timestep if debLevB
2431     * STOP in exf_check_range if 'out of range'
2432     * range chosen generous to allow for potential extema
2433     TBD: a version with stricter range
2434     permitted range would be runtime parameters
2435 jmc 1.390 o GMredi:
2436     - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
2437     - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
2438     - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
2439 mlosch 1.388 o GCHEM:
2440     - move call to GCHEM_FORCING_SEP, so that it is now called before
2441     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
2442     - introduced a useGCHEM runtime flag and applied it everywhere.
2443 mlosch 1.392 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
2444     this flag is now only visible within GCHEM-pkg routines.
2445     - moved gchem_forcing_int temporarily into ptracers_forcing, this will
2446     be replaced by a 3D array that is computed before thermodynamics; for
2447     this, the tracer ID iTracer had to be included into the parameter list
2448     of ptracers_forcing
2449 mlosch 1.394 - set up forward_step to call gchem_forcing, that will replace
2450 mlosch 1.392 gchem_forcing_int in ptracers_forcing
2451     - cleaning up
2452 jmc 1.389 o small cleaning of exch2: remove files that are also in eesupp/src
2453 mlosch 1.387
2454 heimbach 1.386 checkpoint56
2455 jmc 1.385 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
2456 edhill 1.384 o mnc: cleanup "full" files--fixes out-of-memory problem
2457 heimbach 1.386 o ECCO-GODAE
2458     * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
2459     * fully merged and updated from SIO code
2460     windstress sign change affects
2461     - exf_inscal_[u/v]stress
2462     - sign of xx_tau[u/v] adjustments
2463     - signs in cost_scat
2464     * ctrl_get_gen: avoid update of tau[u/v] for first few days
2465     * natl_box_adjoint updated and compressed
2466     * 2-level checkpoint switch added
2467     (tested in EXP. 1 of natl_box_adjoint)
2468     * new switch doInitXX to avoid init. of xx_... in optimcycle=0
2469     o SVD
2470     * first complete, non-hacked version for SVD calculations
2471     * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
2472     performed via direct access files admtlm_vector.it????
2473     (via ctrl_[un]pack)
2474     * optimcycle is used for ARPACK iteration counter
2475     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
2476     * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
2477     and add linear transforms where necessary
2478     * controls are initial/final SST, SSS (can be extended; need to check
2479     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
2480     o mdsio: filename info to both stderr, stdout
2481     o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
2482     from sign change
2483 edhill 1.384
2484 jmc 1.383 checkpoint55j_post
2485 jmc 1.382 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
2486     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
2487 edhill 1.381 o add consistent build directories and .cvsignore files to verification
2488 dimitri 1.380 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
2489 edhill 1.379 o make all subroutines 30 or less characters in length for certain older
2490     compilers to work (a thorough search only turns up two routines in
2491     pkg/ptracers)
2492 jmc 1.378 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
2493     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
2494    
2495 jmc 1.377 checkpoint55i_post
2496 jmc 1.376 o change arrays for total vertical diffusivity (2.D if explicit,
2497     3.D if implicit) ; each ptracer uses its own background value.
2498 edhill 1.375 o added mnc/NetCDF output capability to ocn_compon_interf
2499     - added bits to verification/cpl_aim+ocn so that it can run on
2500     ITRDA and other clusters without the mpirun "-wd" option
2501 afe 1.374 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
2502     configuration
2503 edhill 1.373 o give MNC the ability to create additional files rather than
2504     exceeding a specified file size limit "MNC_MAX_FILESIZE"
2505     - the default is just less than 2GB which is a practical limit
2506     on many systems
2507 jmc 1.372 o Compute the non-local term using either KPP vertical diffusivity (=default)
2508     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
2509 jmc 1.349
2510 jmc 1.371 checkpoint55h_post
2511     o add verification test "vermix"
2512 edhill 1.370 o remove all the *_ioinc flags and replace with the single global
2513     outputTypesInclusive flag
2514 jmc 1.369 o allow to set a vertical profile of vertical diffusivity for T & S
2515 jmc 1.371 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
2516     o useMNC moved from data.mnc to data.pkg
2517 jmc 1.369
2518 heimbach 1.368 checkpoint55g_post
2519     o Renaming carbon AD experiments to comply with testreport conventions
2520     o Updating adjoint of Held-Suarez hs94.1x64x5
2521     o Fixing directives for non-ECCO forward_step, after ECCO directives
2522     have been fixed to avoid recomp. of do_oceanic_phys
2523     Works well for global_ocean.90x40x15,
2524     but recomp. issue remains for carbon
2525     o Updating adjoint output for natl_box_adjoint after
2526     pkg/ecco has been modified (see taga c55d_post)
2527    
2528 edhill 1.367 checkpoint55f_post
2529     o rename to timeave_init_fixed
2530    
2531 heimbach 1.366 checkpoint55e_post
2532     o some delicate re-shuffle of store directives to avoid one
2533     extra call of do_oceanic_physics
2534     affects ecco_the_main_loop.F, do_oceanic_physics.F
2535     checkpoint_lev1_directives.h
2536     o NB: this may break global_ocean adjoint temporarily,
2537     but it is clear how to fix it. Will do later, need this now.
2538    
2539 heimbach 1.365 checkpoint55d_post
2540     o ECCO specific cost function terms (up-to-date with 1x1 runs)
2541     o ecco_cost_weights is modified to 1x1 runs
2542     o modifs to allow observations to be read in as
2543     single file or yearly files
2544     o enable to read exf forcing fields as either
2545     single file or yearly files (flag useExfYearlyFields)
2546     checkpoint55d_pre
2547    
2548     o switch between 2-level and 3-level checkpointing
2549 edhill 1.364 o add ability of MNC to write local and "partial" (eg. 2D slices where
2550     the full 3D field is never actually stored) arrays to NetCDF files
2551     with the correct (that is, the complete multi-dimensional) set of
2552     array indicies
2553     - used in mom_vecinv() to write the diagFreq output
2554     - tested (demonstrated) in verification/aim.5l_cs
2555 edhill 1.363 o further mnc-ification
2556     - add verification/lab_sea to the list with mnc setups
2557     - fix undefined mnc v-names in cd_code
2558     - add kpp to mnc output (both snapshot and timeave)
2559 mlosch 1.362 o non-hydrostatic code
2560     - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
2561     in calc_gw.F
2562     - defaults to viscAh
2563     - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
2564     friction or Leith) in non-hydrostatic mode, as long as there is
2565     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
2566 heimbach 1.360 o pkg/cost
2567     extend simple cost functions to treat time mean quantities
2568     (T,U,V) via cost_accumulate_state from cost_tile
2569 jmc 1.358 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
2570     be 2 times larger than the minimum size the advection scheme requires.
2571     now get a perfect conservation of salt in advect_cs test-exp (updated)
2572 mlosch 1.356 o GGL90 (Gaspar's TKE mixed layer)
2573     - add horizontal diffusion of TKE, requires exchanges in
2574     do_fields_blocking_exchanges, horizontal diffusivity is zero by
2575     default. In OPA there is no horizontal diffusion of TKE but the
2576     mixing coefficients are computed from a horizontal average of TKE of
2577     6 points or so. I think that diffusion has a little more physical
2578     justification.
2579     - clean up ggl90_calc in the hope of reducing memory usage (this hope
2580     was in vain)
2581     - mask tke-variable in ggl90_init
2582 jmc 1.355 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
2583     o fix biharmonic diffusion on CS-grid.
2584 mlosch 1.354 o more obcs stuff
2585     - added obcs_external_fields_load as an alternative to the EXF-pkg option
2586     for reading boundary values. This routine is called from
2587     obcs_prescribe_read
2588     - updated obcs_check
2589 mlosch 1.357 - changed sponge layer relaxation parameter units for days to seconds
2590     - turned off sponge layer by default
2591 heimbach 1.359 - changed argument list of OBCS_CALC to myTime+deltaTclock
2592 mlosch 1.361 - fixed about 35 bugs in obcs_external_fields_load
2593 mlosch 1.354
2594 heimbach 1.353 checkpoint55c_post
2595 heimbach 1.352 o obcs stuff
2596     - new runtime flags useOBCSprescribe, useOBCSbalance
2597     - re-arranged obcs_calc
2598     - moved exf_getobcs to obcs_prescibe_read
2599     obcs_prescibe_read is called after ORLANSKI stuff
2600     and independent of it (executable can contain all).
2601     - updated obcs_check
2602 heimbach 1.353 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
2603     These may be necessary only if tangential velocities are
2604     prescribed at OB, not sure, needs testing.
2605 edhill 1.351 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
2606     which simplifies the calls and passes the ifc check-bounds test
2607    
2608 jmc 1.350 checkpoint55b_post
2609     o add a 2D scalar, Z location, exchange_2 routine.
2610 jmc 1.349 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
2611     to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
2612     affects advect_cs results (for the wrong reason): update output.txt
2613 jmc 1.348 o use a more standard discretization for biharmonic viscosity ;
2614     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
2615     affects results of dome set-up: update output.txt
2616     o fix gad_advection.F (CubedSphere part), back to version 1.23
2617     o fix bug in mom_vi_del2uv.F (CubedSphere part).
2618 mlosch 1.341
2619 heimbach 1.347 checkpoint55a_post
2620     o merged code to
2621     * prescribe/read time-dependent open boundaries
2622     (works in conjunction with exf, cal)
2623     * sponge layer code for open boundaries
2624     * each boundary N/S/E/W now has its own CPP option
2625     (healthy for the adjoint)
2626    
2627 heimbach 1.346 checkpoint55
2628     o up-to-date adjoint of previous breaks
2629     - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
2630     - global_ocean_ebm: adjoint still needs fix (TLM ok)
2631     - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
2632     - carbon: * remove tr1-related adjoint verification
2633     * add ptracer as control variable
2634     o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
2635     (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
2636    
2637 heimbach 1.345 checkpoint54f_post
2638     o in verification/carbin/ remove experiment related to
2639     ALLOW_PASSIVE_TRACER (array tr1 etc)
2640     code_ad/ input_ad/ results_ad
2641    
2642 mlosch 1.344 o add two new packages
2643     - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
2644     + subject to optimization (memory)
2645     - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
2646     + subject to reordering (many GOTOs in the original code)
2647     + so far opps is called for every (i,j) point, and then operates in
2648     the vertical; one may want to reorder the scheme in order operate in
2649     horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
2650     fields)
2651 edhill 1.343 o overhaul of IO so that we now have flags for MDSIO and/or MNC
2652     - all verification tests compile and run with linux_ia32_g77
2653     - defaults are compatible with current input files--nothing
2654     should change if you were not previously using MNC
2655     - MNC output has been added in numerous places (eg. timeave)
2656     but there are still a few writes not yet do-able with MNC
2657     (this is in progress)
2658     - flags now allow for either/or/both use of MDSIO and MNC and
2659     documentation will soon follow
2660     - numerous small formatting cleanups for ProTeX
2661 edhill 1.342 o add version info (via BUILD_INFO.h) to MNC and stdout
2662    
2663 mlosch 1.341 checkpoint54e_post
2664     o add two new packages
2665     - pp81 (Packanowski and Philander, 1981), Richardson number and
2666     stratification dependent mixing
2667     - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2668     - these scheme operate in a similar manner as KPP (without ghat, of
2669     course), however there is only one diffusivity that is used for both
2670 mlosch 1.1068 temperature and salinity (and passive tracers)
2671 stephd 1.340 o add offline package
2672 edhill 1.339 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2673     provided by Stephanie Dutkiewicz
2674 edhill 1.338 o genmake2: add ability to search for C compilers and cleanup test output
2675     - fixes recent SX-6 problems and should help with others (eg. HP-UX)
2676    
2677 jmc 1.337 checkpoint54d_post
2678 adcroft 1.336 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
2679 jmc 1.337 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
2680     leading to additional shift by 5 days each year of integration
2681     (i.e. leading to considerable offset over the years)
2682 jmc 1.335 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
2683     o start with no AB and no initial filtering (staggerTimeStep):
2684     change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
2685     o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
2686     (external loading & cpl import/export stay in forward_step.F)
2687     o update coupling interface to work with new staggerTimeStep
2688     o change MDSIO ptracers_pickup.
2689 jmc 1.334 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
2690 edhill 1.333 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
2691 jmc 1.334 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
2692 edhill 1.333
2693 jmc 1.332 checkpoint54c_post
2694 jmc 1.331 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
2695     this affects (truncation error) output.txt of test-exp:
2696     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
2697     o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
2698 jmc 1.330 o change Qnet to always be the net heat flux, (+upward).
2699     affects (truncation error) output of natl_box exp.: updated
2700 jmc 1.329 o define the max number of passive tracers in PTRACERS_SIZE.h
2701     o start to test mnc routinely in exp0
2702     o add sea-ice loading (sIceLoad) as a new forcing field.
2703    
2704 jmc 1.328 checkpoint54b_post
2705 edhill 1.327 o add testreport "-j JOBS" option for parallel builds (tested and pretty
2706     impressive on Altix and Opteron systems)
2707 edhill 1.326 o diagnostics can now write NetCDF files through the mnc package
2708 jmc 1.325 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
2709 jmc 1.324 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
2710 jmc 1.323 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
2711     affects (truncation error) output of lab_sea & natl_box exp.: updated
2712     o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
2713    
2714 jmc 1.322 checkpoint54a_post
2715     o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
2716     o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
2717     o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
2718     o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
2719     + internal_wave (shift in writing cg2d_ini_res)
2720 jmc 1.321 checkpoint54a_pre
2721    
2722 dimitri 1.320 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
2723     - modified verification/lab_sea and natl_box_adjoint accordingly
2724    
2725 heimbach 1.319 checkpoint54
2726 heimbach 1.318 checkpoint53g_post
2727 jmc 1.317 o prepare splitting of thermodynamics: store convect.counter in common block
2728 jmc 1.316 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
2729     output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
2730 dimitri 1.315 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
2731 jmc 1.314 o new parameter "nShapS": allow to treat differently S from T (nShapT)
2732     o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
2733 heimbach 1.318 o restore adjointability
2734 jmc 1.314
2735 jmc 1.313 checkpoint53f_post
2736     o modifications that affect AIM experiment results (update output.txt):
2737     - no advection of S at top interface Nr (pkg/generic_advdiff)
2738     - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
2739 jmc 1.312 o AIM pkg:
2740     - include stability function into surf.Flux derivative relative to Tsurf
2741     - calculate clear-sky radiation & surface temp. change (for diagnostics)
2742 jmc 1.313
2743 afe 1.311 checkpoint53e_post
2744     o merged cylindrical coord configuration
2745     o added rotating_tank experiment
2746 afe 1.310 checkpoint53e_pre
2747    
2748 jmc 1.309 checkpoint53d_post
2749 jmc 1.308 o faulks upgraded: re-generate output.txt that have changed:
2750     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
2751 adcroft 1.307 o Added Bryan and Lewis, 1979, vertical diffusivity profile
2752 jmc 1.306 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
2753 adcroft 1.305 o added Sadourny discretization of Coriolis
2754     - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
2755     - re-enabled use of omega3 (useAbsVorticity)
2756 adcroft 1.304 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
2757 jmc 1.309 vector-invariant equations
2758 adcroft 1.304 - note: does *NOT* yet use same variable visc. for no-slip BC's.
2759 mlosch 1.303 o recoded the lateral boundary conditions for non-hydrostatic w, this time
2760     hopefully without new bugs
2761     - still to do: biharmonic friction for non-hydrostatic w
2762 adcroft 1.302 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
2763     o regenerated output for global_ocean_ebm (using -ieee)
2764 adcroft 1.301 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
2765     of mom_common/
2766     - simple re-arrangement of instructions within computing loop
2767     checkpoint53d_pre
2768 mlosch 1.297
2769 heimbach 1.300 checkpoint53c_post
2770 jmc 1.299 o new version of coupler for AIM+thSIce and Ocean models
2771     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
2772     - land: change Evaporation of snow
2773     - aim with thSIce: fix bug in snow-precip.
2774 mlosch 1.297 o changes to calc_gw.F
2775     - bug fix for w^2 term near the bottom boundary
2776     - (hopefully) improve the lateral slip boundary condtions for use with
2777     partial/looped cells
2778     - because the bug fix changes two verification experiments anyway (exp5
2779     and plume on slope), change the lateral boundary condition from half slip
2780     to the value of no_slip_sides
2781 heimbach 1.298 o ebm package wasnt quite up to the parallel task. Fixed that.
2782 heimbach 1.300 o Adjoint of EBM package + verification
2783     * TLM OK
2784     * ADM not sufficient accuracy yet (needs further testing)
2785 heimbach 1.295
2786 heimbach 1.296 checkpoint53b_post
2787     o Commiting new energy balance model to repository
2788     * package is pkg/ebm
2789     * verif. is verification/global_ocean_ebm
2790     * references are in ebm_driver.F
2791     C * X. Wang, P. Stone and J. Marotzke, 1999:
2792     C Global thermohaline circulation. Part I:
2793     C Sensitivity to atmospheric moisture transport.
2794     C J. Climate 12(1), 71-82
2795     C * X. Wang, P. Stone and J. Marotzke, 1999:
2796     C Global thermohaline circulation. Part II:
2797     C Sensitivity with interactive transport.
2798     C J. Climate 12(1), 83-91
2799     C * M. Nakamura, P. Stone and J. Marotzke, 1994:
2800     C Destabilization of the thermohaline circulation
2801     C by atmospheric eddy transports.
2802     C J. Climate 7(12), 1870-1882
2803     o Will need long integration testing.
2804 heimbach 1.295 checkpoint53b_pre
2805 dimitri 1.292
2806 adcroft 1.294 o created pkg/mom_common in preparation for variable viscosity code
2807     o renamed and split ini_mnc_io
2808 jmc 1.293 o pkg/land: only liquid water can diffuse or run-off
2809     o AIM using land: soil wetness availability account for snow
2810 dimitri 1.292 o added printMapIncludesZeros to EEPARMS namelist
2811 heimbach 1.290
2812     checkpoint53a_post
2813     o restore TAMC compatiility for exf_constants.h
2814     (no usage of _d in .h)
2815     o Additional storing in KPP in an attempt to fix
2816     TAMC problem with adjoint of KPP code.
2817     (no success...)
2818     Identical code works fine with TAF.
2819 dimitri 1.291 o Fixed verification/natl_box_adjoint experiments.
2820     Initial conditions for Experiments 4 and 5 are now
2821     set to "SEAICE_initialHEFF=0", which is more reasonable,
2822     and hence gives results closer to that of Experiment 2.
2823     Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
2824 cnh 1.289
2825     checkpoint53
2826     o stable checkpoint with up to date adjoint
2827     TLM tests only run for 1st grdchk at the moment. Its unclear if
2828     this is a code problem or a problem with resetting code for g_
2829     variables that is being autogenerated wrong.
2830     Otherwise:
2831     o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
2832     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
2833     are both still in chaos following their security messes.
2834 jmc 1.279
2835 edhill 1.288 checkpoint52n_post
2836     o various build (mostly genmake2) changes including:
2837     - ability to build/run more easily within Cygwin and MacOS X
2838     - more complicated Makefiles with a stronger dependence on Gnu Make
2839 dimitri 1.285 o pkg/seaice modifications
2840 dimitri 1.287 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
2841     of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
2842     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
2843 dimitri 1.285 - changed proxy for geostrophic velocity and updated
2844 dimitri 1.286 verification/lab_sea/results/* accordingly
2845 dimitri 1.285 - removed ADI dynamic solver from pkg/seaice
2846     - replaced all occurrences of 1/CSTICE or 1/CSUICE
2847     they caused a segmentation fault under certain circumstances
2848 mlosch 1.283 - removed unused field WATR
2849 mlosch 1.282 o bug fix in exf-package:
2850     - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
2851     now reflect that.
2852 mlosch 1.281 o small fixes in the cal-package:
2853     - set reference date to first of January for the 'model'-calendar
2854     - failing of cal_CheckDate in cal_FullDate now actually results in a
2855     warning
2856 mlosch 1.280 o small modifications in exf-package to increase flexibility:
2857     - change climtempfreeze from a constant to a runtime parameter that
2858     is specified in data.exf_clim (default = -1.9)
2859     - introduce runtime parameter windstressmax (default = 2.0) that is
2860     specified in data.exf
2861 jmc 1.279 o fix in pkg/thsice:
2862     - update Evap (Tsf changes) to be consistent with Latent heat flux
2863     - maintain snow precipitation unchanged (even if Tsf >=0).
2864     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
2865 edhill 1.272
2866 jmc 1.278 checkpoint52m_post
2867 mlosch 1.277 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
2868     this does not change any of the results, because myIter=0 in swfrac always
2869     lead to jwtype=2 (the default anyway), but the call makes little sense
2870     as a default
2871 jmc 1.276 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
2872 jmc 1.275 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
2873     atmospheric model (AIM) to use it ; add a "slab ocean" component.
2874     o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
2875     o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
2876 dimitri 1.274 o extending useSingleCpuIO option to work with new exch2 I/O format
2877     - old-style, missing-tile I/O is still accessible by defining CPP
2878     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
2879 edhill 1.273 o monitor package can write to NetCDF files and/or STDOUT
2880     o fix re-definition bug in MNC_GRID_INIT_ALL()
2881 edhill 1.272 o doc/api_reference added
2882     - a framework for building an API Reference Manual using all
2883     the "protex" comments embedded in the code
2884     - see pkg/generic_advdiff, pkg/mnc for examples
2885 edhill 1.269 o MNC:
2886     - make myThid the last argument for all subroutines
2887     - new default for the grid files: NO halos
2888 edhill 1.270 - add useMNC and other run-time flags
2889     - separate per-file-group handling of the unlimited dimension
2890     - early initialization of MNC w/ flags read at the eeboot stage
2891     and lookup tables set in initialize_fixed
2892     - write all MNC output to a freshly-created directory
2893 jmc 1.268 o thermodynamics sea-ice (thsice) is now tested with testreport.
2894     o test exp. advect_cs: use the standard cs32 grid ; update output.
2895 heimbach 1.271 o Added functionality to grdchk:
2896     pick global i,j,k position (or nearest wet) where to perform check.
2897 jmc 1.266
2898 jmc 1.267 checkpoint52l_post
2899     o new land formulation:
2900     a) use ground enthalpy as prognostic variable to ensure exact
2901     energy conservation.
2902     b) account for water temperature and for latent heat of freezing
2903     in all processes (rain, run-off, ground storage)
2904     c) compute surface and ground temperature implicitly.
2905     o aim_v23 modification for new land model:
2906     a) Treat separately land / ocean / sea-ice surface fluxes
2907     to allow implicit computation of land & sea-ice surface temp.
2908     b) add snow precipitation.
2909 jmc 1.266 checkpoint52l_pre
2910    
2911 jmc 1.265 o fix problem (when 1 tile is empty) in min/max monitor.
2912     o fix bug in timeAve (u,vZetatave in common block)
2913 dimitri 1.264 o no restoring terms under ice for pkg/seaice
2914 dimitri 1.263 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
2915     o bug fix for pkg/seaice pickups
2916 edhill 1.262 o change MNC call locations and add coordinate attributes
2917 jmc 1.260 o mask vorticity at the corner ; affects global_ocean.cs output
2918     o fix ini_curvilinear_grid ; test CS experiments with mpi
2919 jmc 1.259 o aim.5l_cs: modify sea-ice fraction input file ; update output
2920 heimbach 1.261 o exf: Adding simple range check routine for exf fields after read
2921 adcroft 1.256
2922 heimbach 1.257 checkpoint52k_post
2923 adcroft 1.256 o removed top-level directory "diags"
2924     - we migrated these functions to pkg/timeave a long time ago
2925     o fixed bug introduced in pkg/monitor
2926 heimbach 1.257 o accuracy ctrlprec = 32 insuffient for gradient checks using
2927     averaged fields (I/O via cost_averages)
2928     -> use ctrl.h in active_file*.F to control I/O precision.
2929     o paramter list of CALL ADTHE_MAIN_LOOP
2930     o added initial do_the_model_io to ecco
2931     o set all ...Freq to zero after cost_final
2932     taveFreq, dumpFreq, pChkptFreq
2933 heimbach 1.258 o MAIN and ECCO differentiability restored
2934 heimbach 1.255
2935     checkpoint52j_post
2936     o fix nchklev in tamc.h for global_ocean...
2937     o Bringing flow and store directives up-to-date
2938     o Really weird thing!
2939     call do_the_model_io from the_main_loop with parameters
2940     starttime, niter0, instead of mytime, myiter, screws up the adjoint:
2941     TAF places a faulty re-call of initialise_varia
2942     after cost_final call which should not be there!
2943     checkpoint52j_pre
2944 jmc 1.253
2945 afe 1.254 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
2946     error messages
2947 jmc 1.253 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
2948 afe 1.252 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
2949     debug output
2950 afe 1.251 o modfied mdsio_writefield.F to handle non-global files under exch2
2951 jmc 1.250 o update AIM Cubed-Sphere exp (aim.5l_cs):
2952     use land, p*, and Franco.M forcing fields with fractional land-sea mask.
2953     o update AIM Equatorial Channel exp:
2954     use standard aim_v23 pkg and change the SST fields to be more realistic.
2955 afe 1.248 o globalFile now works with exch2
2956 afe 1.247 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
2957 jmc 1.253 mon_vort3.F to make exch2 friendly with >1 tile per cube face
2958 dimitri 1.249 o limit timeave output for hi-res integrations
2959 adcroft 1.245
2960     checkpoint52i_post
2961     o removed CPP_EEOPTIONS.h from verification/*/code
2962     o updated the tiling for global_ocean_pressure
2963     checkpoint52i_pre
2964 jmc 1.246
2965     o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
2966     the old pkg/aim).
2967 afe 1.239
2968 dimitri 1.244 checkpoint52h_pre
2969 afe 1.243 o shortened offending lines in exch2_send_rx?.template
2970 afe 1.242 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
2971 edhill 1.240 o genmake2: add build & execute test for NetCDF code
2972 afe 1.239 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
2973     old grid files, moved CPP_EEMACROS.h to pkg/exch2
2974 dimitri 1.238 o added useSingleCPUIO flag to monitor.F and mon_out.F
2975 dimitri 1.241 o added temporary hack for sea-ice dynamics on the cube:
2976     metric terms are ignored and it is assumed that
2977     there is no sea-ice on cube faces 1, 2, 4, and 5.
2978 dimitri 1.238
2979     checkpoint52f_post
2980 afe 1.236 o added exch2 cube routines to pkg/exch2
2981     o modified hs94.cs-32x32x5 to use it
2982     o added new grid files to hs94.cs-32x32x5
2983 dimitri 1.238 checkpoint52f_pre
2984 dimitri 1.228
2985 jmc 1.235 checkpoint52e_post
2986 jmc 1.234 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
2987     for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
2988 jmc 1.235 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
2989     to work with implicit vertical advection and AB ;
2990     o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
2991     o update output (gad_calc_rhs.F changes affect truncation error) of exp:
2992     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
2993 jmc 1.233 checkpoint52e_pre
2994    
2995     o fix bug in impldiff when Nr=1 or Nr=2.
2996 jmc 1.232 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
2997     o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
2998 jmc 1.229 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
2999     ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
3000 dimitri 1.228 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
3001 dimitri 1.231 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
3002     o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
3003 jmc 1.220
3004 jmc 1.226 checkpoint52d_post
3005 adcroft 1.230 o re-tiled many expts to allow comparison in multi-processor mode
3006     - updated output accordingly
3007     - changed hs94.128x64x5 to use intial T from file rather than use the
3008     random number generator
3009 molod 1.227 o add infrastructure in model routines for fizhi and gridalt packages
3010 jmc 1.220 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
3011 dimitri 1.222 o changes to permit hi-res, cubed-sphere, configuration
3012     - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
3013     - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
3014     - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
3015     of surface winds for the cube
3016     (A verification experiment, based on global_ocean.cs32x15, but with
3017     pkg/seaice turned on and with on-the-fly interpolation from the NCEP
3018     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
3019     complete with example surface forcing files and matlab scripts to look
3020     at the output and compare it with that of global_ocean.cs32x15.)
3021 jmc 1.223 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
3022     but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
3023     to conform to the common rule.
3024 jmc 1.224 o check-in the first version of the coupler + interfaces for multi-components
3025     set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
3026     - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
3027     - atmosphere: use pkg aim_v23 ; no sea-ice for now.
3028     - ocean and atmos. share the same horizontal grid (no interpolation).
3029     - exchanges between component and coupler is done in forward_step
3030 jmc 1.225 o new verification experiment, cpl_aim+ocn:
3031     coupled ocean - AIM atmosphere on cs32 grid.
3032 jmc 1.217
3033 dimitri 1.219 checkpoint52d_pre
3034 jmc 1.217 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
3035 jmc 1.218 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
3036 heimbach 1.213
3037 heimbach 1.216 checkpoint52c_post
3038 heimbach 1.213 o Fixing OPTIONS files for use of exf:
3039     - ALLOW_ECCO not needed
3040     - ECCO_CPPOPTIONS.h should not be included from
3041     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
3042     as has been the case in the past
3043     - All cal/exf related options are currently set in
3044     single header file. Should remain so until we
3045     agree on a consistent new policy.
3046 heimbach 1.214 o Removed all CPP options for cal package.
3047     cal has no more CPP options.
3048 heimbach 1.215 o modified STOREs in GAD_ADVECTION
3049     o corrected key comp. for passkey
3050 heimbach 1.210
3051 jmc 1.212 checkpoint52b_post
3052     o new version: "thsice" of thermodynamic sea-ice pkg:
3053     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
3054     - modify fluxes but do not change theta directly;
3055     - light cleaning of bulk_force pkg (still needed with thsice).
3056     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
3057     + output_thsice.txt to test thsice & bulk_force pkgs.
3058     o put back grid & coriolis monitor output.
3059 jmc 1.211 checkpoint52b_pre
3060    
3061     o call "do_the_model_io" at the beginning (=> dump initial state)
3062     o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
3063 heimbach 1.210 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
3064     (need info on NUMBER_OF_PTRACERS)
3065     o missing PTRACERS headers in some routines
3066     o default tamc.h in pkg/autodiff supposed to crash
3067     to ensure proper customization
3068 dimitri 1.206
3069 heimbach 1.209 checkpoint52a_post
3070 jmc 1.208 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
3071 dimitri 1.207 - moved surfaceTendencyTice from pkg/seaice to main code
3072 jmc 1.208 - subroutine FREEZE_SURFACE now limits only surface temperature
3073     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
3074     => new output.txt for global_ocean.cs32x15 & global_with_exf
3075     - keep the old version of FREEZE for backward compatibility;
3076     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
3077 heimbach 1.209 - corresponding modifs for TAF directives
3078 dimitri 1.207 o added surface flux output variables to TIMEAVE_STATVARS
3079     o time-averaged output for pkg/ptracers
3080 heimbach 1.209 o fix problem with ECCO-related divided adjoint
3081     snapshot file was missing some ad-variables,
3082     but no warning issued by TAF
3083 dimitri 1.206
3084 dimitri 1.207 checkpoint52a_pre
3085 dimitri 1.206 o some bug fixes for #undef REAL4_IS_SLOW
3086 heimbach 1.205
3087     checkpoint52 = ecco_c52_e35
3088     o after testing adjoints of checkpoint51u_post
3089 edhill 1.203
3090 heimbach 1.204 checkpoint51u_post
3091     o this is the post-merge tag of the ecco-branch
3092     (needs another clean checkout and re-testing)
3093     o various natl_box_adjoint configs and results
3094     but no input fields
3095     o obcs adjoint not yet merged!
3096     o adding ECCO global 1x1 and 2x2 degree configs
3097     o updated/extended some store directives for seaice
3098     o pkg/ecco now containes ecco-specific part of cost function
3099     o top level routines the_main_loop, forward_step
3100     supersede those in model/src/
3101     previous input data.cost now in data.ecco
3102     (new namelist ecco_cost_nml)
3103     o in ctrl/ cleaned some cross-dependencies and updated CPP options
3104    
3105     checkpoint51t_post
3106     o this is the pre-merge tag of the ecco-branch
3107    
3108 edhill 1.203 checkpoint51s_post
3109     o cleanup: removed various obsolete #define-s
3110 heimbach 1.204 o pkg/grdchk
3111     - renamed 'ph-grd 3' to 'grad-res'
3112     - merged from ecco-branch
3113     (remaining bug fixes for obcs gradient checks)
3114     - additional high-precision output for testreport
3115     (grep for 'precision_grdchk_result')
3116 edhill 1.202
3117     checkpoint51r_post
3118     o cleaned up or removed CPP_OPTIONS.h files
3119     o updated results for some of the tests to reflect the new
3120     optfiles (-ieee: -O0 instead of -O3)
3121 heimbach 1.201
3122     checkpoint51q_post
3123     o cd_code:
3124     - moved cd_scheme.F -> cd_code_scheme.F
3125     - separate read_checkpoint from cd_code_ini_vars.F
3126     - separated cd_code part from write_checkpoint
3127     - updated AD_SOURCE, generated .flow
3128     - added CD_CODE_VARS.h to the_main_loop
3129     - Moving cd_code specific store dir.s to pkg/cd_code
3130     o ctrl package totally restructured
3131     - pack/unpack now optional and decoupled from
3132     xx_/adxx_ I/O
3133     - ctrl_pack/unpack cleaned
3134     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
3135     - confined inclusion of AD_CONFIG.h to where necessary.
3136     o genmake2: changed AD dependencies from SRCFILES to AD_FILES
3137 edhill 1.198
3138 edhill 1.200 checkpoint51p_post
3139 edhill 1.198 o create initial cd_code package
3140 edhill 1.199 - WARNING: the initialization of fields within packages
3141     is broken because INI_FIELDS (where READ_CHECKPOINT is
3142     called) is called *before* PACKAGES_INIT_VARIABLES.
3143     This seems to be backwards since
3144     1) its important to initially zero the entire field including
3145     the "halo" region
3146     2) zeroing needs to be done *before* reading pickup info
3147     and the pickup call might or might not happen in any
3148     particular run
3149     - this needs an overhaul for R2
3150 edhill 1.198 o cleanup verification/*/code/GMREDI_OPTIONS.h
3151     o cleanup testreport
3152 heimbach 1.196
3153     checkpoint51o_post
3154     o bringing AD-related verif's up to date with genmake2
3155     - carbon/
3156     - global_ocean.90x40x15/
3157     - hs.94.1x64x5/
3158     - (front_relax/ )
3159     o (more) consistent directory structure for AD-related verif.'s
3160     o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
3161     o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
3162     o bug fix in find_alpha.F for MDJWF:
3163     - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
3164     change rho -> rho-rhoConst
3165     - replace call find_rho to find_rhonum
3166     o initialisation of rFlx extended to full array (required by TAF)
3167     and shifted to thermodynamics
3168     o removed PTRACERS.h in ptracers routine
3169     o added surfacetendencyPtr to S/R parameter list pracers_forcing
3170     o Correcting initialisations for fVerU, fVerV.
3171     o helping TAF to recognize dependency on kUp for
3172     fVerU, fVerV
3173     o Replacing delZ by delR in pkg/ctrl/
3174     checkpoint51o_pre
3175 dimitri 1.192
3176 edhill 1.195 o undid all of cp51 pending some cleanups and discussion
3177 heimbach 1.197 o added the [#include "AD_CONFIG.h"] statement to all files that need
3178     it for adjoint/tl #defines
3179     o re-worked the build logic in genmake2 to support AD_CONFIG.h
3180     o removed tools/genmake since it no longer works
3181 dimitri 1.194
3182     checkpoint51n_post
3183     o modifications to make FREEZE flux visible to pkg/kpp
3184     - moved surfaceTendencyTice from pkg/seaice to main code
3185     - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
3186     - subroutine FREEZE now limits only surface temperature
3187     (this means new output.txt for global_ocean.90x40x15,
3188     global_ocean.cs32x15, and global_with_exf)
3189     o added surface flux output variables to TIMEAVE_STATVARS
3190    
3191     checkpoint51n_pre
3192 dimitri 1.192 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
3193 edhill 1.193 o added [#include "AD_CONFIG.h"] to all files that use the following
3194     defines:
3195     - ALLOW_ADJOINT_RUN
3196     - ALLOW_TANGENTLINEAR_RUN
3197     - ALLOW_ECCO_OPTIMIZATION
3198 edhill 1.190
3199 edhill 1.191 checkpoint51m_post
3200 edhill 1.190 o incorporating changes to get TAMC/TAF working in genmake2
3201     - added new TAMC/TAF targets to the Makefile
3202     - various cleanups related to package handling
3203 edhill 1.191 - these changes should have no impact on the forward model
3204 dimitri 1.189
3205     checkpoint51l_post
3206     o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
3207     - faster algorithm for cal_addtime.F
3208     - higher precision arithmetic, where needed
3209     - pkg/exf *startdate variables changed from calendar date to
3210     model integration time
3211    
3212     checkpoint51l_pre
3213 jmc 1.188 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
3214     o enable to apply restoring on S & T only in a latitude band.
3215     o update output (external_forcing_surf modif. change truncation errors)
3216     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
3217 edhill 1.186
3218 jmc 1.187 checkpoint51k_post
3219     o change default to: useNHMTerms=.FALSE.
3220     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
3221     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
3222     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
3223     exp1, ideal_2D_oce
3224     - change data file of oceanic exp (leave the results unchanged for now)
3225     exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
3226     o set gravitySign automatically according to the vertical coordinate used
3227     (and change sign: back to "logical" value: +1 when R increases downward)
3228 edhill 1.186 o added an include barrier to the default CPP_OPTIONS.h and
3229     removed the #include "PACKAGES_CONFIG.h" from it
3230 jmc 1.187 o fix a bug in mom_fluxform (from chk51j_post)
3231 heimbach 1.185
3232     checkpoint51j_post
3233     o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
3234     o adjusted some flow directives (dynamics, thermodynamics)
3235     o added cubed-sphere case to test cost function
3236     o heckpoint_lev?_directives.h now include
3237     pkg-specific directives, whenever those are enabled.
3238     o Moving pkg-specific flow directives to corresponding pkg
3239     Moving pkg-specific differentiation list to corresponding pkg
3240     Moving pkg-specific checkpoint-lev storing to corresponding pkg
3241     ---> conventions are
3242     - pkg_ad.flow
3243     - pkg_ad_diff.list
3244     - pkg_ad_check_lev?_dir.h
3245 stephd 1.181
3246 edhill 1.184 checkpoint51i_post
3247     o merge of the branch-genmake2
3248     - knowingly breaks the older genmake
3249     - automatic generation of all ALLOW_${PKG_NAME} defines
3250     - new testreport supersedes older testscript
3251     o large number of package inclusion and header cleanups
3252     checkpoint51i_pre
3253    
3254 edhill 1.183 o new output for adjoin of global ocean vector invariant
3255     o fix for checkpoint of thermodynamic seaice and bulk_force
3256     o Steph gchem various cleanups
3257    
3258 stephd 1.181 checkpoint 51h_pre
3259 edhill 1.183 o fixed some single quotes
3260 stephd 1.181 o modify gchem pkg to be more versatile
3261     o modifications to clean up dic pkg
3262     o add pkg/cfc
3263 heimbach 1.182
3264     checkpoint51g_post
3265     o provide links for ARPACK and ADM*TLM
3266     o start removing verification/vero/
3267     o update AD-related stuff
3268     (in particular some IF-statements in model/src/ routines)
3269     o adding to verification/global_ocean.90x40x15/ adjoint of
3270     vector invariant setup
3271 dimitri 1.177
3272 heimbach 1.180 checkpoint51f_post
3273 jmc 1.179 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
3274 dimitri 1.178 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
3275 dimitri 1.177 of tracer Green's fucntions for ocean inversion project.
3276 dimitri 1.175
3277 dimitri 1.176 checkpoint51f_pre
3278 dimitri 1.175 o Added on-the-fly spatial interpolation capability
3279     "USE_EXF_INTERPOLATION" to pkg/exf.
3280 dimitri 1.176 - This is a temporary Cartesian-grid hack until
3281 dimitri 1.175 the super-duper ESMF coupler becomes available.
3282 dimitri 1.176 - See verification/global_with_exf/README for usage example.
3283     - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
3284     flags and modified pkg/seaice accordingly.
3285 dimitri 1.175 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
3286     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
3287     non-local transport term.
3288 heimbach 1.172
3289 jmc 1.174 checkpoint51e_post
3290     o pkg/mom_vecinv:
3291     - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
3292     - add time-ave diagnostic of vorticity advection.
3293     o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
3294     o atmospheric geopotential: - include water vapor effect;
3295     - use p^kappa in p* scaling.
3296 jmc 1.173 o land pkg: read initial state from files.
3297     o AIM : add stratospheric drag in the upper level
3298    
3299 heimbach 1.172 checkpoint51d_post
3300 jmc 1.173 o change function ILNBLNK (=> last non-blank char.) to return zero
3301     (instead of the string length) when the string. char is empty
3302 jmc 1.171 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
3303 heimbach 1.172 o modif's to restore TAMC compatibility
3304     - avoid "_d" constructs in PARAMETER declarations
3305     - avoid interrupting lines by comment lines
3306     o Use cluster local disks for purely local I/O
3307     vs. globally visible disks needed for ctrl stuff
3308     (merged from ecco-branch)
3309     - new active_file_loc... and mdsio_..._loc routines
3310     - affected packages: autodiff, ctrl, grdchk, mdsio
3311 heimbach 1.169
3312 heimbach 1.170 checkpoint51c_post
3313     o introducing integer flag debugLevel
3314     - debLevZero: suppress all output
3315     - debLevA: standard
3316     - debLevB: equivalent to current debugMode=.TRUE.
3317     o introducing pathname variable mdsioLocalDir for mdsio
3318     that can be specified at runtime
3319     (relevant for cluster I/O to local disk)
3320     `
3321 heimbach 1.169 >>>checkpoint51b_post
3322     adjoint of ptracers
3323     o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
3324     o extended state in checkpoint_lev?, etc.
3325     o alternative ctrl/cost with tr1 or ptracer
3326     o new comlev1_bibj_ptracers
3327     o new ptracers.flow
3328     o made ptracers_forcing same as external_forcing_s
3329     o added verification for adjoint with ptracers
3330     - adm. grdchk fail so far
3331     - tlm. grdchk OK
3332     - checked tapelev/comlev recomputations: OK
3333     <<<checkpoint51b_pre
3334 stephd 1.168
3335     checkpoint51a_post
3336     o added code for biogeochemistry package
3337     - new pkgs: dic, gchem
3338     - new subroutine in ptracers
3339     o modify code for biogeo packages
3340     - in model/src and pkg/ptracers
3341 heimbach 1.166
3342     checkpoint51
3343     o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
3344     - autodiff, ctrl, exf, grdchk, seaice
3345     kept separate packages
3346     - cost, ecco, obcs
3347 heimbach 1.167 o updating verification/internal_wave, verification/lab_sea
3348     (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
3349 heimbach 1.165
3350     checkpoint50i_post
3351     o Preparing next differentiable checkpoint and sync
3352     of MAIN vs. ecco-branch
3353     - 1st step: this one is differentiable
3354     - 2nd step: next(! not this) checkpoint will have updated packages
3355     from ecco-branch)
3356 jmc 1.161
3357 heimbach 1.164 checkpoint50h_post
3358 jmc 1.163 o new package "land": provide surface BC for AIM.
3359     o pkg/ptracers: apply exchange to all tracers after reading a pickup.
3360 jmc 1.161 o AIM: use true log-P extrapolation for near surface temp (= as in
3361     F.Molteni paper) ; update aim.5l_cs output.
3362 adcroft 1.162 o New variable in PARM03 for more flexible pickups
3363 heimbach 1.164 o somewhat cleaned package initialisation sequence for
3364     ctrl/ cost/ ecco/ in packages_... routines
3365 dimitri 1.160
3366     checkpoint50g_post
3367     o merged with release1_p17 (pkg/seaice and verification/lab_sea)
3368     - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
3369     - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
3370     made the default because of faster convergence than ADI
3371 heimbach 1.159
3372     checkpoint50f_post
3373     o exf totally restructured
3374     - replaced all exf_set_ routines by one generic exf_set_gen.F
3375     and made sure it's still differentiable
3376     - split exf_getffields.F into new exf_bulkformulae.F
3377     - exf_inscal_/exf_outscal_ suffixes consistent with field names
3378     - updated adjoint/makefile and relevant verif. accordingly
3379 adcroft 1.156
3380 heimbach 1.158 checkpoint50f_pre
3381 jmc 1.157 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
3382     + change Evap over land. (update aim.5l_cs output)
3383 adcroft 1.156 o added missing .cvsignores and made uniform across expts
3384     o changed configuration of tidal_basin_2d expt
3385     o added pkg/debug functions for tracing code in fatal crashes
3386     o tidied pkg/monitor to use MONITOR_OPTIONS.h
3387     o new fn in pkg/monitor to stop model if solution grows too big
3388     o removed lots of single quotes from comments
3389    
3390 mlosch 1.155 checkpoint50e_post
3391     o make KPP work with PTRACERS
3392     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
3393     nearly a copy of kpp_transport_s
3394     - there is no analogue to SurfaceTendencyS, so I have to use
3395     gPtr(of the surface layer) instead
3396     o add a new platform SunFire+mpi (SunFire 15000) to genmake
3397     checkpoint50e_pre
3398    
3399     checkpoint50d_post
3400 mlosch 1.154 o change kpp output from multiple-record state files to single-record state
3401     files analogous to write_state.F
3402     o reduce the output frequency of cg3d-related stuff to the monitor frequency,
3403     analogous to the cg2d-related output.
3404 mlosch 1.155 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
3405     so that writing to internal file fn (with length 512) fails.
3406 mlosch 1.154 checkpoint50d_pre
3407 jmc 1.151
3408 jmc 1.153 checkpoint50c_post
3409     o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
3410 jmc 1.152 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
3411 jmc 1.151 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
3412     o bug fixed in convective adjustment diagnostic (multi-tile set-up).
3413     o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
3414 dimitri 1.150
3415     checkpoint50c_pre
3416     Merging from release1_p13:
3417     o bug fix for pkg/seaice dynamic solver
3418     o Added SEAICE_initialHEFF to pkg/seaice
3419 jmc 1.149
3420     checkpoint50b_post
3421     o store u*,v* in gU,V instead of in guNm1,gvNm1
3422     o in order to put the momForcing out of the Adams-Bashforth:
3423     move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
3424     to timestep.F
3425     o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
3426     o re-generate output for highly sensitive test-exp:
3427     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
3428 heimbach 1.146
3429 jmc 1.148 checkpoint50b_pre
3430 jmc 1.147 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
3431 heimbach 1.146 o corrected CPP option mismatch in exf_Bulk... functions for case
3432     #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
3433 heimbach 1.145
3434     checkpoint50a_post
3435     o Bug fix for merging between c50 and KPP.
3436     ikey was passed from thermodynamics to kpp_calc via
3437     common block rather than being recomputed in kpp_calc,
3438     in contradiction with new key itdkey.
3439     New key ikppkey created, and tamc.h headers updated.
3440 heimbach 1.143
3441 heimbach 1.144 checkpoint50
3442     - 2nd step of merge with ecco-branch:
3443     merge changes in ecco-branch back into main trunk
3444     - bug fix in find_alpha
3445     - more storing in gmredi_calc_tensor.F, kpp_routines.F
3446     - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
3447     - merged some sliced AD support routines
3448    
3449 heimbach 1.143 checkpoint49
3450     merged from ecco-branch:
3451     o exf:
3452     - Enable initialisation of forcing fields to constant
3453     (runtime) values.
3454     - in exf_getffields.F
3455     Reduce i-/j-loop to interior domain, discarding overlaps.
3456     That also fixes wrong TAF-key computations for key_1, key_2
3457     with bulf formulae.
3458     - exf_init.F modify #ifdef for exf_init_evap
3459     - exf_getffieldrec.F, ctrl_getrec.F
3460     The following INT-usages are not safe:
3461     fldsecs = int(fldsecs/fldperiod)*fldperiod
3462     fldcount = int(fldsecs/fldperiod) + 1
3463     and were modified.
3464     o autodiff: checkpoint_lev...
3465     - updated storing for bulk formulae (some arrays were missing)
3466     - added state for seaice package
3467     - synchronized with main branch
3468     o DIVA:
3469     Modif.s in
3470 heimbach 1.144 - the_main_loop.F
3471     - the_model_main.F
3472 heimbach 1.143 and added cost_final_restore.F cost_final_store.F
3473     o With these changes, it is possible to fully separate
3474     the first forward run to compute the cost function (mdthe_main_loop)
3475     and adjoint runs over individual DIVA intervals (adthe_main_loop)
3476     into separate model executions.
3477     This enables better tuning of DIVA to given queue sizes.
3478     o Loss of cost function value in consecutive DIVA runs is
3479     fixed by storing to 'costfinal' file.
3480     o Appropriate call of ctrl_unpack/_pack,grdchk_main at
3481     beginning/end of adjoint integration is accounted for.
3482     The current changes apply to TAF-1.4.26.
3483     TAF has one remaining bug, requiring one manual change
3484     (see MITgcm manual).
3485     o cal: synchronized between MAIN and ecco-branch
3486 heimbach 1.141
3487 heimbach 1.142 checkpoint48i_post
3488 heimbach 1.141 o Changes to restore differentiability of code w.r.t. previous tag
3489     (mostly adding new routines to make list and replacing
3490     pressure by totPhiHyd).
3491     o Updated and merged grdchk package
3492     - has both ADM and TLM checks
3493     - works for single- and multi-proc.
3494     - output cleaned
3495     - worked successfully for parallel DIVA
3496     o genmake:
3497     - Adding -platform=SP4
3498     - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
3499     o Modif. for DIVA:
3500     ctrl_unpack should not be called in intermediate DIVA interval.
3501     (similar thing would apply for active files such as
3502     tbar, sbar, psbar, which should not be reinitialised;
3503     only relevant for ecco-branch)
3504 dimitri 1.136
3505 heimbach 1.140 checkpoint48h_post
3506 jmc 1.137 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
3507 dimitri 1.136 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
3508     o Added SEAICE_initialHEFF to pkg/seaice
3509 dimitri 1.139 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
3510 jmc 1.135
3511     checkpoint48g_post
3512     --- EOS:
3513     o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
3514     store total Potential in totPhyHyd for diagnostics & EOS.
3515     o fix restart and overlap Pb when using Z-coord and EOS funct. of P
3516     --- Pressure/geopotential gradient:
3517     o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
3518     o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
3519     ( changes results of global_ocean_pressure )
3520     o NLFS + z-coord.: add eta*Rho' contribution.
3521     o accurate phiHyd when using interface-W at the middle between 2 centers
3522     ( changes results of ideal_2D_oce )
3523     o includes r* 2nd term in potential gradient.
3524 dimitri 1.134
3525     checkpoint48f_post
3526     Merging from release1_p12:
3527     o Modifications for using pkg/exf with pkg/seaice
3528     - improved description of the various forcing configurations
3529     - added basic radiation bulk formulae to pkg/exf
3530     - units/sign fix for evap computation in exf_getffields.F
3531     - updated verification/global_with_exf/results/output.txt
3532     o Added pkg/sbo for computing IERS Special Bureau for the Oceans
3533     (SBO) core products, including oceanic mass, center-of-mass,
3534     angular, and bottom pressure (see pkg/sbo/README.sbo).
3535     o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
3536     to avoid negative values in shallow regions.
3537     - updated verification/natl_box/results/output.txt
3538     - updated verification/lab_sea/results/output.txt
3539     o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
3540     o Added useSingleCpuIO option (see PARAMS.h).
3541     o Updated useSingleCpuIO option in mdsio_writefield.F to
3542     work with multi-field files, e.g., for single-file pickup.
3543     o pkg/seaice:
3544     - bug fix in growth.F: QNET for no shortwave case
3545     - added HeffFile for specifying initial sea-ice thickness
3546     - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
3547     o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
3548     kpp_transport_t.F, forward_step.F, and the_main_loop.F
3549     o pkg/seaice:
3550     - adjoint-friendly modifications
3551     - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
3552 jmc 1.131
3553 jmc 1.133 checkpoint48e_post
3554 jmc 1.131 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
3555 jmc 1.132 o dynamics: change definition of computational domain & adapt mom_fluxform
3556     accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
3557     o following exp works with Olx=Oly=2 (and pass through checkbounds option):
3558     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
3559 jmc 1.133 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
3560 jmc 1.132 global_ocean.90x40x15 global_with_exf global_ocean_pressure
3561     inverted_barometer solid-body.cs-32x32x1
3562     (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
3563 jmc 1.130
3564     checkpoint48d_post
3565     o in preparation for r*:
3566     a) use pre-computed gradient of hydrostatic potential:
3567     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
3568     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
3569     => affects results of glob_oce_pressure (different truncation error)
3570     update output.txt of ideal_2D_oce & global_ocean_pressure
3571 jmc 1.129
3572     checkpoint48d_pre
3573     o in preparation for r*:
3574     new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
3575     pass the 2 comp. of the grad. as arguments to momentum S/R.
3576     but for the moment, only used if it does not change the results.
3577     o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
3578 jmc 1.126
3579 heimbach 1.128 checkpoint48c_post
3580     Modifications in treatment of initial flux forcing controls
3581     to avoid extra storing of flux fields.
3582    
3583     checkpoint48c_pre
3584 adcroft 1.127 o Added tidal_basin_2d experiment (currently 1D!)
3585 jmc 1.126 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
3586 jmc 1.124
3587 jmc 1.125 checkpoint48b_post
3588 jmc 1.124 o r* coordinate added in #ifdef NONLIN_FRSURF block.
3589     (modification to pressure gradient not yet implemented)
3590     o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
3591     (for U & V) that are used for vertical advection of momentum.
3592 jmc 1.123
3593     checkpoint48a_post
3594     o In preparation for r*, use temp. array to compute vertical transport
3595     in flux-form momentum pkg. => change results of few test-exp.
3596     Update output of: exp4, exp5, front_relax, global_ocean_pressure,
3597     lab_sea, natl_box & plume_on_slope
3598 jmc 1.122
3599     checkpoint48
3600     o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
3601 heimbach 1.121
3602     checkpoint47j_post
3603 jmc 1.120 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
3604 heimbach 1.121 o moved adexch from forward_step to addummy_in_stepping
3605     o added exch in ctrl_map_...
3606     o aveFreq.=0. at end of cost_final to avoid overwrite in
3607     reverse checkpointing loop
3608     o Yet more changes in gmredi:
3609     * adgmredi_calc_tensor
3610     avoiding all recomputation of gmredi_slope_limit
3611     * adgmredi_x/y/rtransport
3612     added flag for excessive storing to avoid recomp. of
3613     u/v/rtans, dTdx/y/z
3614     -> this is not really necessary and very memory-consuming
3615     * adgmredi_slope_psi:
3616     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
3617     * gmredi_slope_limit
3618     re-activated full calculation of taperfct for case 'ac02'
3619     o updating verification/ adjoints of carbon, global_ocean.90x40x15
3620 heimbach 1.116
3621 jmc 1.119 checkpoint47i_post
3622     o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
3623     o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
3624     default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
3625     o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
3626     o gmredi: fix few bugs.
3627    
3628 adcroft 1.118 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
3629 heimbach 1.116 This will be a good checkpoint to plug into the ecco-branch.
3630     o few modif.'s to get latest version adjointed
3631     (mainly kick out code in ini_linear_phisurf)
3632     o modif's to run adjoint with exactConserv
3633     o case GM_BOLUS_ADVEC should be cleaned
3634     S/R gmredi_slope_psi should be cleaned
3635     o verification/carbon now has exactConserv=.TRUE.
3636 jmc 1.114
3637 heimbach 1.115 checkpoint47g_post
3638 jmc 1.114 o time-average AIM output: becomes independent from statvars time-average
3639     (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
3640 heimbach 1.115 o After TAF bug fix:
3641     Tested adjoint of gmredi package.
3642     Tests were done with checkpoint47 rather than with latest
3643     checkpoint47f_post since the latter is broken for the adjoint
3644     verification/carbon/ contains both ADM and TLM gradient checks.
3645     Here they are, before they get changed/lost/stolen.
3646     Mostly modif.'s to fix numerical sensitivities.
3647     Gradient checks OK for
3648     - GM_taper_scheme:
3649     * clipping
3650     * ac02
3651     * linear
3652     * glw91
3653     * dm95
3654     * ldd97
3655     - GMREDI_OPTIONS:
3656     * GM_VISBECK_VARIABLE_K
3657     * GM_NON_UNITY_DIAGONAL
3658     * GM_EXTRA_DIAGONAL
3659     * GM_BOLUS_ADVEC
3660     in conjunction with data.gmredi parameters to be checked in
3661     in a few minutes under verification/carbon/code/
3662 cheisey 1.112
3663 dimitri 1.113 checkpoint47f_post
3664     Merging from release1_p10:
3665     o modifications for using pkg/exf with pkg/seaice
3666     - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
3667     and SEAICE_EXTERNAL_FLUXES
3668     - pkg/exf CPP options EXF_READ_EVAP and
3669     EXF_NO_BULK_COMPUTATIONS
3670     - usage examples are Experiments 8 and 9 in
3671     verification/lab_sea/README
3672     - verification/lab_sea default experiment now uses
3673     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
3674    
3675 cheisey 1.112 checkpoint47e_post
3676     o created a tag prior to creating a branch
3677    
3678 mlosch 1.111 checkpoint47d_post
3679     o fixed bug in the oceanic pressure coordinates code: vertical viscosity
3680     at the bottom boundary had an erroneous half slip boundary condition
3681     o added bottom drag and no slip boundary condition capabilities to
3682     oceanic pressure coordinates code
3683     o added new verification experiment global_ocean_pressure, this experiment is
3684     also described in the tutorial section of the manual
3685     checkpoint47d_pre
3686 cheisey 1.110
3687     checkpoint47c_post
3688     o Added a verification experiment for a global cubed-sphere ocean run
3689     - verification/global_ocean.cubed32x32x30
3690     - uses pkg/therm_seaice and pkg/bulk_forcing
3691 jmc 1.109
3692     o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
3693     o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
3694     when using P-coordinate; only implemented for atmospheric config.
3695     o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
3696     NOTES: requires option NONLIN_FRSURF to be "#define".
3697     o update advect_xz/results/output.txt (left from checkpoint44g_post)
3698 dimitri 1.108
3699     checkpoint47b_post
3700     Merging from release1_p9:
3701     o pkg/seaice
3702     - removed GOTO's and added taf directives
3703     - double precision constants to reduce the g77 (Linux)
3704     to F77 (SGI) differences reported in release1_p8
3705     o tools/genmake
3706     - added SGI options
3707     o verification/testscript
3708     - updated to that of checkpoint47a_post
3709     o verification/global_ocean.90x40x15/input/eedata
3710     - modified for SGI f77 compatibility
3711     o verification/lab_sea
3712     - added description of sea-ice model
3713     - added missing matlab routines
3714     - added test of thermodynamics parallelization
3715 jmc 1.105
3716 jmc 1.106 checkpoint47a_post
3717 jmc 1.105 o new pkg: aim_v23
3718     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
3719     for now, keep the same surface forcing as before.
3720     - Part-Cell implemented into AIM; check that Heat & Water are conserved
3721     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
3722     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
3723     o add diagnostic of surface correction term in monitor output
3724 jmc 1.106
3725     o bulk_force and therm_seaice
3726 cheisey 1.107 - Two packages: bulk_force (Bulk forcing)
3727     and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
3728     - Earlier integration from Stephaine Dutkiewicz
3729     and Patrick Heimbach.
3730     - Two ifdef statements for compile time,
3731     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
3732 heimbach 1.104
3733     checkpoint47
3734     differentiable version of checkpoint46n_post
3735     o bug fix in quasihydrostaticterms
3736     o * "clean" adjoint code (in terms of extensive recomputations)
3737     can now be obtained for all GMREDI options (i.e. for
3738     - GM_VISBECK_VARIABLE_K
3739     - GM_NON_UNITY_DIAGONAL
3740     - GM_EXTRA_DIAGONAL
3741     - GM_BOLUS_ADVEC )
3742     * However, wrong gradient check problem remains unsolved.
3743     * New CPP options have been introduced for different
3744     tapering schemes
3745     o external_fields_load now part of differentiation list
3746     o pressure needs multiple storing;
3747     would be nice to have store_pressure at beginning or
3748     end of forward_step, e.g. by having phiHyd global (5-dim.)
3749     (NB: pressure is needed for certain cases in find_rho,
3750     which is also invoked through convective_adjustment).
3751     o recomputations in find_rho for cases
3752     'JMD95'/'UNESCO' or 'MDJWF' are OK.
3753     o #define ATMOSPHERIC_LOADING should be differentiable
3754     o ini_forcing shifted to begining of initialise_varia
3755     o Incorporating QNVS line search routines into MITgcm
3756     (this is separate code, and therefore not under pkg)
3757     lsopt/, optim/
3758     o Updated verification/carbon/
3759     - #define GM_VISBECK_VARIABLE_K
3760     - GM_taper_scheme = 'ldd97'
3761 heimbach 1.103
3762     checkpoint46n_post
3763     Merging from release1_p8:
3764     o verification/natl_box:
3765     updating new external_fields_load routine
3766     o New package: pkg/seaice
3767     Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
3768     The sea-ice code is based on Hibler (1979-1980).
3769     Two sea-ice dynamic solvers, ADI and LSR, are included.
3770     In addition to computing prognostic sea-ice variables and diagnosing
3771     the forcing/external data fields that drive the ocean model,
3772     SEAICE_MODEL also sets theta to the freezing point under sea-ice.
3773     The implied surface heat flux is then stored in variable
3774     surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
3775     kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
3776     non-local transport term. Because this call precedes model
3777     thermodynamics, temperature under sea-ice may not be "exactly" at
3778     the freezing point by the time theta is dumped or time-averaged.
3779     N.B.: fairly large differences in accuracy occur across
3780     different platforms/compilers; comparison between
3781     g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
3782     generated output gives:
3783     T S U V
3784     C D M c m s m s m s m s
3785     n p a R g m m e . m m e . m m e . m m e .
3786     f n k u 2 i a a d i a a d i a a d i a a d
3787     g d e n d n x n . n x n . n x n . n x n .
3788    
3789     Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
3790     o GAD:
3791     - generated new common blocks to account for call of
3792     same gad routines with differing traceridentities
3793     (needed to modify tracerIdentity indices in GAD.h)
3794     - generated separate common blocks for case useCubedSphereExchange
3795     (Department of Futurology)
3796     - parameter lists to gmredi_?transport: added tracerIdentity
3797     - added new key indices to tamc.h
3798     o external_fields_load:
3799     - added this routine to TAF list
3800     - needed to make some common blocks global and additional storing
3801     along the same lines as exf package (checkpoint_lev?_directives.h)
3802     o exf:
3803     updated external forcing package
3804     - bug fixes carried over from ecco-branch
3805     (missing OBCS_OPTIONS.h in two routines)
3806     - enable easy to use "no forcing".
3807     - added exf I/O for atmospheric loading
3808     - added exf I/O for runoff data
3809     - transfered scaling between exf <-> MITgcm to exf namelist
3810     o Adding new verification experiment global_with_exf.
3811     This verification experiment is almost identical to the
3812     global_ocean.90x40x15 experiment, except that it uses
3813     the exf (and cal) package instead of the
3814     external_fields_load routine (cf README file).
3815 adcroft 1.94
3816 adcroft 1.102 checkpoint46m_post
3817 adcroft 1.101 o modified testscript to return -- when there are no lines of "%MON" output
3818 adcroft 1.100 o added new flag "quasiHydrostatic" for QH mode
3819     and new routine quasihydrostaticterms()
3820 adcroft 1.99 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
3821     New routine: mom_u_coriolis_nh()
3822 adcroft 1.98 o fixed sign of non-hydrostatic metric terms in u and v equations.
3823     Depend on correct sign of gravitySign.
3824 adcroft 1.97 o added work.pc* to .cvsignore in aim directories using ifc
3825 adcroft 1.96 o introduced flag for controllin non-hydrostatic metric terms
3826 adcroft 1.95 o removed gravitySign from PARM04
3827 adcroft 1.94 o switched to g77/ifc from pgf77 in aim experiments
3828 mlosch 1.93
3829     checkpoint46l_post
3830     o made convective adjustment work with pressure coordinates:
3831     - changed the direction of k-loop in convective_adjustment.F for the
3832     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
3833     - adjusted the reference pressure k-index in convective_adjustment.F
3834     - adjusted the convection condition in convect.F (in analogy to
3835     calc_ivdc.F)
3836     - convective_adjustment no longer computes anything on the halos
3837     - removed the warnings about negative salinity from find_rho.F and
3838     find_alpha.F; instead the new routine look_for_neg_salinity, called
3839     at the beginning of find_rho, find_alpha, and find_beta, does a
3840     check of the entire slice, if CPP-option
3841     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
3842     checkpoint46l_pre
3843 mlosch 1.91
3844 mlosch 1.92 checkpoint46k_post
3845 mlosch 1.91 o fixed the verification/global_ocean.90x40x15 experiment:
3846     - new bathymetry (the world according to A., JMC, and M.)
3847     - new initial fields and forcing fields (*.bin files)
3848     - new POLY3.COEFFS (for the next release one should switch to a full
3849     equation of state: JMD95P or MDJWF)
3850     - fixed several errors and redundancies in the data file
3851     - experiment uses looped cells
3852     - added matlab directory with diagnostic scripts for plotting of output
3853 jmc 1.90
3854     o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
3855     - read AIM physics parameters from a file (data.aimphys)
3856     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
3857 jmc 1.89
3858     checkpoint46j_post
3859     o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
3860     o move wVel computation at the end of the time step, in S/R integr_continuity
3861     o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
3862     o update timeave pkg for wVel diagnostic.
3863     checkpoint46j_pre
3864 mlosch 1.87
3865 jmc 1.88 checkpoint46i_post
3866     o Clean up AIM package (and keep the results unchanged):
3867     include CPP_OPTION and use IMPLICT NONE in all routines ;
3868     declare all the variables _RL ; use _d 0 for all numerical constants.
3869     use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
3870 mlosch 1.87
3871     checkpoint46h_post
3872     o cleaned up the use of rhoNil and rhoConst.
3873     - rhoNil should only appear in the LINEAR equation of state, everywhere
3874     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
3875     and the dynamical equations are all divided by rhoConst
3876     o introduced new parameter rhoConstFresh, a reference density of fresh
3877     water, to remove the fresh water flux's dependence on rhoNil. The default
3878     value is 999.8 kg/m^3
3879     o cleanup up external_forcing.F and external_forcing_surf.F
3880     - can now be used by both OCEANIC and OCEANICP
3881     checkpoint46h_pre
3882    
3883     Added code to convert surface volume flux (fresh water) into
3884     a mass flux when using P coordinates in the ocean (OCEANICP).
3885     Note: It assumes you have set rho0=rhoConst=density of fresh water.
3886 mlosch 1.86
3887     checkpoint46g_post
3888     o Include a new diagnostic variable phiHydLow for the ocean model
3889     - in z-coordinates, it is the bottom pressure anomaly
3890     - in p-coordinates, it is the sea surface elevation
3891     - in both cases, these variable have global drift, reflecting the mass
3892     drift in z-coordinates and the volume drift in p-coordinates
3893     - included time averaging for phiHydLow, be aware of the drift!
3894     o depth-dependent computation of Bo_surf for pressure coordinates
3895     in the ocean (buoyancyRelation='OCEANICP')
3896     - requires a new routine (FIND_RHO_SCALAR) to compute density with only
3897     Theta, Salinity, and Pressure in the parameter list. This routine is
3898     presently contained in find_rho.F. This routine does not give the
3899     correct density for 'POLY3', which would be a z-dependent reference
3900     density.
3901     o cleaned up find_rho
3902     - removed obsolete 'eqn' from the parameter list.
3903     o added two new verification experiments: gop and goz
3904     (4x4 degree global ocean, 15 layers in pressure and height coordinates)
3905     checkpoint46g_pre
3906 heimbach 1.85
3907     checkpoint46f_post
3908     o Enable tangent linear (forward mode) gradient checks:
3909     - extended active file handling to g_... files
3910     - added TANGENT_SIMULATION to theSimulationMode
3911     - extended grdchk package accordingly
3912     o added tangent linear setup in verification/carbon/code_ftl
3913     o added adjoint setup in verification/front_relax/code_ad
3914 mlosch 1.82
3915 cnh 1.84 checkpoint46e_post
3916 mlosch 1.83 o Added new equation of state -> MDJWF
3917     - EOS of McDougall et al., 2002, JAOT, submitted
3918     - caveat: the equation of state is only valid for a smaller (more
3919     realistic?) range of values than JMD95P/Z and UNESCO
3920     - added masks to the calculation of pressure in store_pressure
3921     - added more check values for density in check_eos (ini_eos.F), some of
3922     the old check values are out of the range of the MDJWF-eos, so don't
3923     expect perfect matches for those
3924 cnh 1.84 checkpoint46e_pre
3925 mlosch 1.83
3926 mlosch 1.82 checkpoint46d_post
3927     o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
3928     'OCEANICP', also initialised field pressure correctly in ini_eos in the
3929     case of pressure coordinates. eosType='JMD95Z' in
3930     combination with buoyancyRelation='OCEANICP' now causes an error.
3931     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
3932     in find_alpha/beta.
3933     checkpoint46d_pre
3934    
3935     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
3936     so that JMD95Z and JMD95P give approptiate static stability in find_rho.
3937 adcroft 1.81
3938     checkpoint46c_post
3939     o Changes necessary for ocean in p-coordinates
3940     - Added new buoyancy relation = 'OCEANICP'
3941     - Added new parameters = gravitySign (this used to be contained inside
3942     the factor dRdZ which I added when we first switched to R coordinates).
3943     X GM/Redi is not compatible (yet)
3944     X bottom drag and no-slip need to be debugged.
3945     checkpoint46c_pre
3946 mlosch 1.80
3947     checkpoint46b_post
3948     o Added new equation of state -> JMD95Z and JMD95P
3949 mlosch 1.83 - EOS of Jackett and McDougall, 1995, JAOT
3950 mlosch 1.80 - moved all EOS parameters into EOS.h
3951     - new routines ini_eos.F, store_pressure.F
3952     o Added UNESCO EOS, but not recommended because it requires
3953     in-situ temperature (see JMD95)
3954     o Modified formatting for knudsen2.f in utils/knudsen2 and added
3955     unesco.f to be used with POLY3
3956     checkpoint46b_pre
3957 mlosch 1.79
3958     checkpoint46a_post
3959     o Added (atmospheric) pressure loading
3960     - new field in FFIELDS.h, etc...
3961     - new cpp flag ATMOSPHERIC_LOADING
3962     o Changed hFacC to _hFacC in calc_phi_hyd.F
3963     o Added SHORTWAVE_HEATING to some files for consistency
3964     checkpoint46a_pre
3965 heimbach 1.78
3966     checkpoint46
3967     further merges from release1_p5
3968     o new ctrl package
3969     - adopted from ECCO environment to enable optimization
3970     - added Eliassen Palm fluxes to controls
3971     o added Eliassen Palm flux controls to gradient check package
3972     o cost package
3973     - Compatible with new ctrl package
3974     - added Eliassen Palm cost hooks
3975     - modif's of existing cost functions
3976     o Adjoint-related bug fixes in kpp:
3977     - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
3978     - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
3979     o autodiff package
3980     - flow directives:
3981     + new for S/R do_the_model_io
3982     + enhanced for S/R checkpoint
3983     + new gmredi.flow
3984     - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
3985     disable adcommon.h/g_common.h by default.
3986     - fixed problem for adjoint of global_max
3987     o modified verification/carbon/
3988     o New setup for adjoint of global_ocean
3989     o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
3990     o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
3991     o incorporated hooks for sponge layer code (external_forcing.F)
3992    
3993 jmc 1.77 checkpoint45d_post
3994     o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
3995 jmc 1.76 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
3996     (affects plume_on_slope "cg2d" output)
3997 jmc 1.77 o add new parameter deltaTfreesurf for free-surface time stepping
3998     o exchange gT,gS when using staggerTimeStep & GM & Oly<4
3999 jmc 1.75 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
4000 jmc 1.74 o change phiMin in exp1 (to agree with documentation)
4001     o add new flags:
4002     - T,S forcing inside/outside Adams-Bashforth
4003     - turn off temp,salt advection and/or forcing
4004     - for each tracer, define internal flag for multiDimAdvection & A-B
4005     o monitor: change definition of KE to check conservation of Energy
4006 heimbach 1.73
4007     checkpoint45c_post
4008     o Removed f90 comments ("!")
4009     o Modified initialisations to enable exf package for MITgcm
4010     (without invoking ECCO_PACKAGE).
4011     o modifications to gradient check package (Martin Losch)
4012     - enable centered differences
4013     - modified format of standard output
4014 heimbach 1.72
4015     checkpoint45b_post
4016     o cleaned exchange calls in cg2d
4017     o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
4018     o included CPP option SINGLE_LAYER_MODE in thermodynamics
4019     to configure barotropic setup (Martin Losch)
4020     o moved some initialisations within bi,bj loop in dynamics
4021     (TAF flow dependency)
4022     o in initialise_varia, moved call packages_init_variables
4023     before convective_adjustment_init
4024     (corresponding adjustment of TAF tape initialisation).
4025     o in calc_diffusivity/calc_viscosity extended domain to full overlap.
4026 jmc 1.70
4027 jmc 1.71 checkpoint45a_post
4028     o compute Rho over the whole domain (extend iMin,jMin indices)
4029     o specific exchange for X-slice domain (case Ny=1)
4030 jmc 1.70 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
4031     o solve_for_pressure : set cg2d_x to zero where OBCS are applied
4032 jmc 1.67
4033 heimbach 1.69 checkpoint44h_post = checkpoint45
4034     o Fix to restore differentiability:
4035     place at which packages_init_variables is called in
4036     initialise_varia is crucial for reverse control flow.
4037     o modifications in GMRedi to enable stable adjoint
4038     (corresponding modif's in thermodynamics, dynamics)
4039     o added missing hook for sponge layer code in external_forcing
4040     o modified test cost functions
4041     o storing in gad_advection (plus removal of write(0,*)!
4042     o missing headers TR1.h added in convective_adjustment routines
4043     o errorMessageUnit set non-equal zero in eeboot
4044     (conflict on some platforms, e.g. IBM SP3)
4045     o modified carbon verif.
4046    
4047     checkpoint44h_pre
4048 jmc 1.68 o vertical grid option: allow to put the Interface at the middle between
4049     2 cell-centers ; replace delZ in pkg/kpp by drF.
4050 jmc 1.67 o GM Advective form: Tracers are advected using the residual transport (=
4051     Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
4052 jmc 1.66
4053     checkpoint44g_post
4054     o fix surface correction term in multiDimAdvection (affects plume_on_slope
4055     results) ; ifdef missing in thermodynamics.F
4056 adcroft 1.65
4057     checkpoint44f_pre,checkpoint44f_post
4058     o added PTRACERS package
4059     This allows an arbitrary number of passive tracers to be integrated
4060     forward simultaneously with the dynamicaly model.
4061     + Implemented so far:
4062     - basic forward algorithm (time-stepping, advection, diffusion, convection)
4063     - I/O and checkpointing
4064     - GM/Redi *but* using the GM/Redi coefficient of Salt
4065     + Not implemented so far:
4066     - KPP
4067     - OBCS
4068     + No specific example supplied (yet) but global_ocean.90x40x15 has the
4069     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
4070     line in data.pkg.
4071     + This package is disabled by default since it increases storage.
4072    
4073 jmc 1.60
4074 adcroft 1.64 o testscript: added -cleanup option
4075 jmc 1.63 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
4076     b) enable to filter 2D fields.
4077 adcroft 1.62
4078     checkpoint44e_pre,post
4079     o re-wrote convective adjustment to use pre-calculated weights
4080     Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
4081     Adds: model/src/convective_weights.F, convectively_mixtracer.F
4082     Original calls to convect() still in place.
4083 heimbach 1.61
4084     chkpt44d_pre,post
4085     o added missing EXCLUDE_MONITOR flags
4086     o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
4087     (incompatible typ in MIN/MAX expressions caused problems
4088     on IBM SP3)
4089     o in genmake added variable MAKEDEPEND
4090     plus resetting for case SunOS
4091     o added timer_stats.c routine for IBM SP3
4092     o removed variables in dynamics
4093     !!! I forgot to create tag chkpt44d_pre !!!
4094     !!! But chkpt44d_pre = chkpt44c_post !!!
4095 jmc 1.63
4096     o real fresh water flux implemented with non-linear free-surface.
4097 heimbach 1.58
4098 jmc 1.59 chkpt44c_pre,post
4099     o few fix (mask in shap_s2, EmPmR in external_field_load,
4100     USE_NATURAL_BCS in solve_for_P);
4101     o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
4102    
4103 heimbach 1.58 checkpoint44b_pre/_post
4104     o merge of relevant stuff from the ecco-branch:
4105     - genmake: removed $S64 overwrite for case SunOS
4106     - pkg/exf: update and corrections for field swapping and obcs
4107     - pkg/ecco: parameter lists for the_model_main, the_main_loop
4108     harmonized between ECCO and MITgcm
4109     - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
4110     updated checkpointing_lev... lists for obcs
4111     - model/src: minor changes in forward_step, plot_field
4112     added directive for divided adjoint in the_main_loop
4113     - pkg/mdsio: added mdsio_gl_slice
4114 jmc 1.57
4115     o check parameters & config (chkpt44a_pre,post)
4116 jmc 1.56 o OBC and NonLin_FrSurf.
4117    
4118 heimbach 1.55 checkpoint44
4119 jmc 1.54 o fix bug in mom_vi_del2uv
4120 jmc 1.56 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
4121     o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
4122     o update AIM experiments (NCEP input files)
4123     o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
4124 heimbach 1.55 o added some stuff for AD
4125 adcroft 1.53
4126     checkpoint43
4127     o added two new advection tests
4128     o added global 4x4 degree ocean test
4129     o added test of H&S94 with free surface on cube
4130     o some final mods for gradient check, adjoint,...
4131 heimbach 1.52
4132     checkpoint42
4133     Fixed AD-related problems:
4134     o Store directives up-to-date with re-arranged Adams-Bashforth
4135     (mainly thermodynamics.F)
4136     o New store directives for multi-dim. advection schemes
4137     * new CPP flag ALLOW_MULTI_DIM_ADVECTION
4138     * new common block and key passkey
4139     (mainly gad_advection.F)
4140     o Modified store directives for split of dynamics/thermodynamics
4141     for the case ALLOW_KPP
4142     o Cleaned argument list for timestep_tracer.F
4143 adcroft 1.51
4144     checkpoint41
4145     o re-formatted/added comments in prologues of key subroutines
4146     to work with protex
4147 heimbach 1.47
4148 adcroft 1.50 checkpoint40
4149     o moved calc_gs, calc_gt and calc_tr1 back to model/src
4150     o added FLT (floats) package from Arne along with demo. experiment
4151     o re-arranged Adams-Bashforth scheme for tracers to allow easier
4152     implementation of forward-in-time forcing terms
4153     o more mods for non-linear free-surface including new variable
4154     o modified multi-dim method to work on cube
4155     o bug fix in KPP (from DM)
4156    
4157 adcroft 1.49 checkpoint40pre9
4158     o added DST advection schemes
4159     o fix MPI bug on SGI's
4160     o modifications for non-linear free-surface
4161     o fixed conditionals for fixed flow/passive tracer only mode
4162     o added tension/strain form of stress tensor
4163     o changes to commenting of arguments for TAF/TAMC
4164     o added/updated many matlab scripts
4165 adcroft 1.50 o added multi-dimensional advection method for tracers
4166 adcroft 1.49
4167 adcroft 1.48 checkpoint40pre8
4168 heimbach 1.47 o new package rw/
4169     Added method for dumping intermediate local arrays:
4170     mdsio_writetile - same as mdsio_writefield except works from inside
4171     bi,bj loop
4172     mdsio_writelocal - same as mdsio_writetile except works for local
4173     arrays
4174     write_local_r? - higher-level wrapper for mdsio_writelocal
4175     Controlled by diagFreq. Defaults to zero (ie. no dumps)
4176     Example given at end of mom_vecinv.F that dumps some local arrays.
4177     o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
4178     control flux-form versus vector invariant code.
4179     Switch is runtime flag vectorInvariantMomentum (defaults to false)
4180     or genmake -DISABLE ...
4181     o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
4182     (additional storing is now needed for case vecinv;
4183     currently nothing implemented to switch this storing off
4184     in case fluxform is used since no CPP flag available).
4185 heimbach 1.46
4186     checkpoint40pre7
4187     o bug fix in dynamics.F
4188     calc_viscosity called before k=1,Nr loop.
4189     o added some #ifdef's ALLOW_PASSIVE_TRACER
4190     o cleaned initialisations in ctrl_map_ini
4191     related to TAF
4192 heimbach 1.45
4193     checkpoint40pre6
4194     o split dynamics into thermodynamics & dynamics
4195     o corresponding split of calc_diffusivity into
4196     calc_diffusivity, calc_viscosity
4197     (kpp_calc_diff, kpp_calc_visc).
4198     o Added diffkr, kapgm to control variables
4199     o bug fix in gmredi_slope_limit for ldd97
4200 adcroft 1.44
4201     checkpoint40pre5
4202     o proper initialization of Adams-Bashforth time stepping
4203     + uses forward step for very first step of model (iter=0)
4204     o re-generated *all* output since almost all output is modified by this
4205     change (sorry but we've been putting this one off for about 2 years)
4206     + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
4207     *not* regenerated since they are already out of date and I don't
4208     want to create the impression that they are suddenly working.
4209     o removed KAP stuff for DEC's
4210     o modified/added many .cvsignore files in */code and */input
4211     o added new expt "solid-body.cs-32x32x1"
4212     + this uses an alternative form of ini_curvilinear_grid.F which
4213     is not necessarily any better than the current one...
4214 heimbach 1.43
4215     checkpoint40pre4
4216     o added re-initialisations of utrans,vtrans,rtrans in
4217     calc_common_factors which are crucial for TAF.
4218     o extended iMin,jMin range for calc_common_factors,
4219     calc_diffusivity
4220     o added option ALLOW_PASSIVE_TRACER
4221     o a few minor updates and fixes
4222    
4223 heimbach 1.42 checkpoint40pre3
4224     o created calc_gtr1.F for gad package
4225     o split the_main_loop and re-introduced forward_step
4226     o some recomputations of nIter0 for TAMC
4227    
4228 heimbach 1.41 checkpoint40pre2
4229     o Updated to latest branch of AJA, JMC
4230     o Added gradient check package
4231     o Added routines for passive tracer handling
4232     o Added carbon sequestration sensitivity experiment
4233    
4234 heimbach 1.39 checkpoint39
4235     o Modifications and fixes to support TAMC
4236     (mainly missing or wrong directives)
4237     o Corrected common blocks when fooling TAMC to produce adjoint I/O
4238     in addummy_in_stepping
4239     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
4240     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
4241     o Included following packages:
4242     cal: calendar
4243     exf: external forcing
4244     ecco: essential routines to control use of cal, exf
4245     (NB: this is not the full ECCO environment)
4246 heimbach 1.40 o disabled some packages by default in genmake
4247 heimbach 1.39
4248 heimbach 1.38 checkpoint38
4249     o see notes_c37_adj.txt
4250     o corrected wrong layer index in external_forcing_t
4251     o replaced the_main_loop/forward_step by the_main_loop
4252     o removed forceoutput from write_state
4253     (replaced criteria for initial/final state)
4254     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
4255 jmc 1.36
4256 jmc 1.37 checkpoint37
4257     o mdsio.F routine split and packaged in pkg/mdsio
4258     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
4259     used unless genmake -disable=mdsio)
4260     o allow a more precise surface-geopotential gradient for the atmosphere
4261     taking into account the change in space of Alpha (=1/rho) at the surface.
4262     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
4263     (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
4264     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
4265     Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
4266     [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
4267     o Time-Average diagnostics defined as a pseudo package "timeave".
4268     o pickup files : old pickup (before c35) did not work with new code (c35
4269     and after) unless activating 2 commented lines in initialise-varia.
4270     o Non-Hydrostatic pickup file Pb fixed.
4271     o bug with Rigid-lid version (since c35) fixed.
4272    
4273 jmc 1.36 checkpoint36
4274 jmc 1.37 o implement Crank-Nickelson barotropic time-stepping
4275 jmc 1.36 o recover Time-Average diagnostics
4276     o fix Pb in checkpoint (PR#19)
4277     o AIM become a standard package ; clean unused CPP_kees
4278 jmc 1.35
4279     checkpoint35
4280     o subtantial rewrite of dynamics.f
4281     o allows staggered time-stepping
4282     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
4283     o added bottom drag (linear + quadratic)
4284 heimbach 1.33
4285     checkpoint34
4286     o Modified exchange routines for correct reverse simulation.
4287     o Added verification output to comply with bug fix in impldiff.F
4288     as of c33 (exp2, natl_box).
4289     o Corrected store directives in dynamics.F
4290     o Corrected array boundaries in impldiff.F
4291     o Corrected array dimensions in gmredi.
4292     Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
4293 heimbach 1.34 o Added routine GLOBAL_SUM_INT to global_sum.F
4294 heimbach 1.33 o Added mdsio_gl.F for ECCO purposes.
4295 adcroft 1.32
4296     checkpoint33
4297     o Fixed bug in lower BC in impldiff.F
4298     o Fixed confusion about units of forcing arrays in FFIELDS.h
4299     namely Fu,Fv,Qnet,Qsw,EmPmR:
4300     - Removed verification/natl_box/code/external_fields_scale.F
4301     (did not differ from that in model/src)
4302     - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
4303     (see FFIELDS.h for description)
4304     - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
4305     kpp_calc.F and kpp_transport_t.F
4306     - Removed model/src/external_fields_scale.F and calls to it
4307     - verification/natl_box uses flux data with "atmospheric" sign so
4308     a special version of external_fields_load.F is used to
4309     change the data as it's read in. This way, the arrays
4310     have the right units and signs at all times tha a user could
4311     possibly use them.
4312     o Corrected genmake to delete a temporary file during configuration
4313 heimbach 1.31
4314     checkpoint32
4315     o Scaling of forcing fields moved from external_forcing.F to
4316     external_fields_scale.F, called directly after loading fields.
4317     o Surface relaxation terms added to surface tendency fields in
4318     extra subroutine.
4319     o impldiff.F changed to avoid storing by TAMC of huge intermediate
4320     fields.
4321     o Changes in GMRedi to comply with packaging structure.
4322     o Modifications and bug fixes in KPP package.
4323     o Verification experiment for KPP added (verification/nat_box/)
4324 heimbach 1.30
4325     checkpoint31
4326     o Packages interface brought in line with defined standard
4327     -> new routines packages_...F
4328     -> changes in initialise_fixed.F, initialise_varia.F
4329     -> enables initialisation interface for ECCO package
4330     o Rescaling of external forcing fields immediately after read
4331     (removed from external_forcing.F)
4332     -> new: surface_fields_scale.F
4333     -> affects ini_foorcing.F, external_fields_load.F
4334     o Computation of surface tendencies before tendency updates.
4335     -> new: external_forcing_surf.F
4336     o Change of variable names useGMRedi, useKPP, useECCO
4337     o Further changes in dynamics.F, impldiff.F for TAMC
4338     o Tested for experiments 0, 2, 4.
4339     - not yet tested for GMRedi.
4340     - not yet tested for KPP.
4341 adcroft 1.29
4342     checkpoint30
4343     o Updates for OBCs
4344     o New experiment for test OBCs (internal_wave)
4345     o New output.txt in verification/exp4/results/
4346     o Updates for KPP: calculation of viscosity corrected, new variables
4347     kpp_dumpFreq and kpp_taveFreq
4348     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
4349     and entry for T90 in genmake
4350 adcroft 1.28
4351     checkpoint29
4352     o packaged KPP and GM/Redi
4353 heimbach 1.27
4354     checkpoint28
4355     o Corrected initialization of hFacMin for difference vertical coordinates
4356     o Modified calculation of partial cell thickness to more robust algorithm
4357     o config_summary.F: replaced write_1D_... by write_0D_...
4358     read_write.F: added subroutines write_0D_...
4359     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
4360     included some initialisations required for TAMC.
4361     o routine calc_isoslopes: modified sqrt computation to make it
4362     differentiable for zero argument.
4363     o routines dynamics, impldiff:
4364     included store directives and tape key computations required for TAMC.
4365     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
4366 adcroft 1.26
4367     checkpoint27
4368     o fixed calc_isoslopes() to so that cancellation of terms in tensor
4369     formulation works properly with variable resolution.
4370     o restructured the calling tree between the_model_main() and dynamics()
4371     o split initialise() into initialise_fixed() and initialise_varia()
4372     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
4373     in new routine ini_psurf()
4374 adcroft 1.25
4375     checkpoint26
4376     o moved some #ifdef in optional routines to encompass everything
4377     except the argument declarations. This was using up some memory.
4378     o fixed macros like _ADT to work with both versions of Linux cpp
4379     o cleaned up some unused and uninitialized variables
4380     (helps when debugging with strict compile options)
4381     o split up CPP_EEOPTIONS.h into options and macros
4382     (macros are now in eesupp/inc/CPP_EEMACROS.h)
4383     o patch for 2 processor JAM mode
4384 adcroft 1.24
4385     checkpoint25
4386     o updates for OBCs and NH
4387     o dramatically reduced memory usage
4388     o added "JAM" routines for use on Artic network
4389     o parameterization of convection by implicit vertical diffusion
4390     o added a diagnostic of convective index
4391     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
4392     (this is was partly for OBCs and NH but also in anticipation of
4393     an explicit free-surface option)
4394     o initial state input files for U and V
4395 adcroft 1.23
4396     checkpoint24
4397     o Removed some spurious "REAL"s
4398     o Updated KPP to latest version from JPL
4399     o Added a COS(latitude) in horizontal viscosity
4400 adcroft 1.22
4401     checkpoint23
4402     o Added del^4 diffusion for salt and temperature
4403     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
4404 adcroft 1.21
4405     checkpoint22
4406     o Made many small changes: implicit none, format(i5), etc...
4407     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
4408 adcroft 1.20
4409     checkpoint21
4410     o Introduced new I/O package that supports direct-access records (mdsio.F)
4411     o Split-up mid-level I/O routines
4412     o Updated input data for experiments 0,1,2,4 and 5
4413     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
4414 adcroft 1.18
4415 adcroft 1.19 checkpoint20
4416     o Tidied up open-boundaries some more
4417     o Added non-hydrostatic code
4418     o Fixed some input data
4419     o Modified MPI start-up to work in "coupled" context.
4420    
4421 adcroft 1.18 checkpoint19
4422     o Tidied up directory structure for verification experiments.
4423     o Added new code for open boundaries.
4424     o Corrected advective terms near boundaries.
4425     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
4426     o Implemented free-slip/no-slip BCs and del^4 dissipation.
4427 adcroft 1.19 o Split default parameters out of ini_parms.F into set_defaults.F.
4428 cnh 1.17
4429     checkpoint18
4430     o Further changes for optional code generation with
4431     CPP - ugh!
4432 cnh 1.16
4433     checkpoint17
4434     o Beginning to incorporating modularity
4435     for supporting atmos. and ocean configs.
4436     o Small changes for TAMC complinace
4437     o New ultra simple test case. Barotropic box
4438     configuration "exp0".
4439 cnh 1.15
4440     checkpoint16
4441     o Minor changes to exchange routines to support
4442     accumulation in reverse mode. Adjoint of an
4443     assignment is an addition.
4444     o Changes to support compilation by TAMC (LR(1)
4445     syntax) and by g77 under Linux ( 72 character
4446     limit ).
4447 cnh 1.14
4448     checkpoint15
4449     Rewrote exchange routines to allow
4450     o General tile <-> tile connectivity.
4451     o TAMC reverse mode flag ( is this really needed? )
4452     o Variable width overlap and exchange region widths.
4453     o Hooks for sharing data via DMA, Arctic, Memory Channel,
4454     shmput/shmget, VIA, SYSV shmem and every other cool
4455     communication method.
4456 cnh 1.13
4457     checkpoint14
4458     Consistent isomorphism chages made. These allow dynamical core
4459     to support both pressure and meters as a vertical coordinate.
4460 cnh 1.12
4461     checkpoint13
4462     Release which corrects global_max problem and a couple
4463     of KGM time-averaging diagnostic errors. Also contains
4464     a double-gyre experiment setup as well as the baseline
4465     4 degree global template. The double gyre template is
4466     organised to allow it to be applied automatically to
4467     the baseline configuration.
4468 adcroft 1.11
4469     branch-point-rdot
4470     A few tidy-ups have been made bt the real point of this
4471     check-point (excuse the pun) is to allow a branch to be
4472     made for the purposes of adding the rDot alterations.
4473     I don't want to commit the rDot to the main-trunk until
4474     we've actually tested it...
4475 cnh 1.10
4476     checkpoint12
4477     Tidy up and added generic genmake script (formerly
4478     configure script).
4479     Released to testers.
4480 adcroft 1.9
4481     checkpoint11
4482     Re-arranged initialise() and introduced ini_vertical_grid()
4483     and ini_masks_etc().
4484 adcroft 1.8
4485     checkpoint10
4486     Introduced the configure script.
4487     Separated out the diags package.
4488     Added template for writing time-averages of tile/intermediate quantities.
4489     Updated SIZE.h in exp2 and made the data big-endian.
4490 adcroft 1.7
4491     checkpoint9
4492     MPI fix. Filename changes (meta/data). salbin*y stuff.
4493     General tidy-up.
4494     SST.bin SSS.bin added to verification/exp2
4495 adcroft 1.6
4496     checkpoint8
4497     Inludes time-dependant forcing and time-averaging.
4498     Works at 4x4 and 2.8125x2.8125 global
4499    
4500     checkpoint7-4degree-ref
4501     Branch from checkpoint7. Released for application to
4502     global modeling and general modeling - process studies, regional
4503     model etc..
4504     Configured for verification/exp2 - 4 degree global, two process.
4505 cnh 1.5
4506     checkpoint7
4507     Created by cnh
4508     Simple 4 degree global simulation
4509     configuration.
4510     Includes climatological wind,
4511     hydrography, bathymetry etc
4512     Does not include Heat Flux and E-P
4513 cnh 1.4
4514     checkpoint6
4515     Created by cnh
4516     merged checkpoint5 with CD and
4517     spherical polar code.
4518     Still some problems with GM Redi
4519     abd full topography.
4520 cnh 1.3
4521     checkpoint5
4522     Created by AJA
4523     contains updates to GM Redi
4524     and reordered timestepping loop
4525     for Implicit Diffusion.
4526 cnh 1.2
4527     checkpoint4
4528     Created by cnh
4529     Contains memory saving macros ( _rdxc etc..) for when
4530     grid variations are limited.
4531     Contains polynomial coeffs for EOS and knudsen program
4532     for generation.
4533    
4534 cnh 1.1 checkpoint3
4535     Created by cnh
4536     Added extra flags for runtime options
4537     Added this file
4538     Added implicit free-surface
4539     Added pre-conditioner
4540     Put compare01 into repository ( compare01/... )
4541     Put data and eedata into repository ( verification/exp1 )
4542    
4543     checkpoint2
4544     Created by AJA
4545     Added GM/Redi
4546    
4547     checkpoint1
4548     Created by AJA
4549     Restructured kloop in dynamics.F
4550     Added non-linear EOS
4551    
4552 cnh 1.2 baseline
4553     Original checked in code
4554 cnh 1.1

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