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Revision 1.1928 - (hide annotations) (download)
Sun Oct 6 00:48:15 2013 UTC (10 years, 8 months ago) by jmc
Branch: MAIN
Changes since 1.1927: +5 -1 lines
document pkg/exf changes

1 jmc 1.1928 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1927 2013/09/30 20:06:42 jmc Exp $
2 jmc 1.475 $Name: $
3 cnh 1.1
4     Notes on tags used in MITgcmUV
5     ==============================
6 jmc 1.1601
7 jmc 1.1928 o pkg/exf:
8     - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
9     rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
10     and rename array obsSIce to exf_iceFraction.
11 jmc 1.1927 o tutorial_deep_convection:
12     - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
13     for now all in this exp. code dir.
14     - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
15     testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
16     o eesupp/src:
17     - added SINGLE_DISK_IO option because reading of parameter files on
18     very large number of processors did not work with existing set-up
19    
20 jmc 1.1925 checkpoint64o (2013/09/25)
21     o pkg/atm_phys & atm_compon_interf:
22     - allows for coupling of gray-atmosphere (atm_phys) with ocean.
23 jmc 1.1924 o tools/build_options:
24     - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
25     & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
26     remove CPP setting (was identical to genmake2 default).
27 m_bates 1.1923 o pkg/gmredi & model/src: Some updating and work done on the residual model.
28     - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
29 jmc 1.1924 - fixed up the calculation of the eddy stress and how it is added to the
30 m_bates 1.1923 external forcing via taueddy_external_forcing.F
31     - at the moment, it is very experimental and only works with the variable eddy
32     diffusivity calculated in gmredi_k3d.F
33 jmc 1.1924 o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
34     lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
35     o testreport (& tools/do_tst_2+2):
36     - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
37 jmc 1.1921 o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
38     - remove CPP='cpp -traditional -P' (this is genmake2 default)
39     - add switch (for big setups) to use 'medium' memory-model (but leave it
40     commented out for now). Note: needed with FC 19 to compile big setups.
41 jmc 1.1920 o pkg/atm_compon_interf:
42     - regroup per field origin (model & pkgs) the coupling storage routines
43     (which accumalate in time each coupling field)
44 jmc 1.1921 - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
45 jmc 1.1920 update accordingly + simplify aim_do_physics.F
46    
47 jmc 1.1918 checkpoint64n (2013/08/26)
48 dimitri 1.1919 o pkg/bbl:
49     - update formulation to reduce dispersion of tracer properties in bbl
50     - replaced horizontal and vertical transport parameters with velocities
51     - changes results for verification/global_with_exf.yearly
52 dgoldberg 1.1917 o verification/halfpipe_streamice:
53     - change to matrix construction; update both Fwd & AD output.
54 jmc 1.1916 o verification/tutorial_tracer_adjsens:
55     - OpenAD test: switch to vector-invariant momentum since fluxform with
56     rStar causes problems with OpenAD; update output.
57 jmc 1.1915 o tools:
58 jmc 1.1916 - genmake2: define a common prefix for all temp-file names ; move them
59     to local /tmp disk (but would be easy to move them back);
60     - xmakedepend: apply the same switch for temp-files.
61 jmc 1.1915 o pkg/offline:
62 jmc 1.1916 - changes for use with rStar (NLFS): assume that we continue to provide
63 jmc 1.1915 UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
64     output files) and apply r* scaling at each time-step (function of the time
65     varying Eta field); use normal pickup files (needed for restart with NLFS).
66 jahn 1.1914 o adjoint with OpenAD:
67     - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
68     package openad. This package has to be compiled for all runs with OpenAD
69     instead of specifying code_oad_all as a modification directory.
70     - link the fortran templates from tools/OAD_support to the build directory
71     for preprocessing to avoid conflicts between different setups compiled
72     simultaneously and simplify cleanup.
73 jmc 1.1913 o pkg/exf:
74     - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
75     main model or other pkgs are exchanged in EXF_MAPFIELDS).
76     o model/src:
77     - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
78     (similar to do_fields_blocking_exchanges.F).
79     o tools/genmake2:
80     - remove TAF output src code just before calling staf (when not doing a fresh
81     built, will stop if things go wrong with staf).
82     - fix target "adobj" (left from TAF version-2 transition)
83 jmc 1.1912 o pkg/diagnostics:
84     - add a parameter to track the status of pkg/diagnostics activation;
85     this replace/extend the use of logical param "settingDiags" (to check
86     when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
87     New S/R to print error message and stop when pkgStatus is not right.
88     - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
89    
90 jmc 1.1911 checkpoint64m (2013/08/13)
91 jmc 1.1910 o model/inc:
92     - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
93     8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
94     o pkg/kpp & aim_v23:
95     - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
96 jmc 1.1909 o pkg/seaice:
97     - restore (last time on 2011/12/24) ability to compile pkg/seaice with
98     undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
99 jmc 1.1910 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
100     o eesupp/src:
101     - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
102     in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
103 jmc 1.1908 o switch to TAF version-2:
104     - add flow directives to "freeze" naming convention for ad-routines that
105     are used in I/O routines of adjoint state and associated common blocks
106     that are used in adcommon.h (backward compatible with version-1)
107     - update all ad-optfiles (in tools/adjoint_options + few local to some
108     verification exp) to switch to latest TAF version (currently 2.5.5);
109     merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
110     out except for diva).
111     - the major change with TAF version-2 is that both the differentiated
112     routines and the forward routines (new) are returned as part of the TAF
113     output source code. Update genmake2 accordingly.
114     - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
115     with version-2 when compared to TLM or FWD gradient); other experiments
116     output show minor changes (machine truncation level); update the few AD &
117     TLM output with 12 matching digits only (some prior to version-2 switch).
118    
119 jmc 1.1907 checkpoint64l (2013/08/05)
120 jmc 1.1905 o model/src:
121     - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
122 jmc 1.1906 - main_do_loop.F: no longer includes additional (AUTODIFF) header files
123     when using TAF but only if using OpenAD.
124 jmc 1.1904 o pkg/mom_common+fluxform+vecinv:
125     - always set horiz. viscosity arrays to background value before calling
126     MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
127     only when using variable horiz. viscosity (useVariableVisc=T);
128     - simplify mom_vecinv.F (only 1 block for momViscosity).
129 jmc 1.1903 o pkg/mom_common: variable horiz. viscosity in NH code
130     - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
131     from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
132     - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
133     useBiharmonicVisc & useVariableVisc.
134     - fix old bug (already in 1rst implementation of variable horizontal viscosity
135     in calc_gw.F, version 1.27, 2006/06/20):
136     horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
137     even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
138     - change background horiz viscosity in vertical momentum (gW) to always be
139     viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
140     any type of variable viscosity, e.g., viscAh/4Grid)
141     - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
142     viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing
143     horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
144     default viscAh,viscA4 is zero).
145 jmc 1.1902 o model/src:
146     - extend length of drC & recip_drC from Nr to Nr+1.
147 jmc 1.1901 o Divided Adjoint (DIVA) with MPI:
148     - genmake2: do not create local ./mpi_headers dir when no file to copy into.
149     - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
150     and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
151    
152 jmc 1.1900 checkpoint64k (2013/07/23)
153 jmc 1.1899 o tools/OAD_support:
154 jmc 1.1900 - avoid the need for file "oadtempflile" in insertTemplateDir.bash
155     and remove it from genmake2.
156 jmc 1.1899 o tools/build_options:
157     - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
158     MPI_HEADER_FILES list (let genmake2 find the missing headers)
159 dgoldberg 1.1898 o verification/halfpipe_streamice:
160 jmc 1.1899 - change to driving stress formulation; update both Fwd & AD output.
161     o tools/genmake2 and Divided Adjoint with MPI:
162     - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
163     - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
164     - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
165     Makefile, which is set by genmake2, and check which mpi-headers are needed.
166     Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
167     - update target "CLEAN" (to also remove ./mpi_headers/ dir).
168 jmc 1.1897 o testreport:
169     - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
170     perform additional runs (number of additional runs is "add_DIVA_runs" taken
171     from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
172     o verification/lab_sea (AD test):
173     - change to test Divided Adjoint Run in this set-up (both standard AD test
174     and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
175 jmc 1.1896 o pkg atm_ & ocn_compon_interf:
176     - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
177     staggerTimeStep implementation) and disable (retired) corresponding
178     parameter.
179 jmc 1.1894 o pkg/offline:
180     - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
181     - add S/R OFFLINE_CHECK to print offline parameter summary
182     and stop if loading a file that is not used;
183     - enable to calculate GMRedi tensor, KPP mixing and convective index
184     when the corresponding file(s) is/are not specified (but pkg is used).
185 jmc 1.1895 - comment out resetting of monitorFreq (to endTime) since it still useful
186     for monitoring CFL numbers and checking offline fields.
187 jmc 1.1893 o OpenAD:
188     - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
189     smaller standard output) and generate new (smaller) output (on baudelaire
190     using gfortran with -ieee) for exp. tutorial_tracer_adjsens
191 jmc 1.1892 o model/src:
192     - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
193     (where external_forcing_adjust was called) and change list of arguments;
194     - merge external_forcing_adjust.F into external_forcing_surf.F
195     - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
196     which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
197     previously in file "balance_relax.F", now removed); remove corresponding
198     arrays in FFIELDS.h.
199     - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
200     a hack for getting back surfaceForcingS (loaded from file) when using
201     ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
202     - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
203     (was getting only 11 digits for AD-grad, due to different truncation
204     error in AD code).
205    
206 jmc 1.1891 checkpoint64j (2013/07/04)
207 jmc 1.1890 o pkg/offline:
208     - to enable the use of other features with pkg offline (e.g., obcs),
209     also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
210     - comment out "allowFreezing" (now active) in 2 offline testing exp.
211 dimitri 1.1888 o pkg/exf ALLOW_RUNOFTEMP
212     - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
213 jmc 1.1892 - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
214 dimitri 1.1889 - changes verification/global_ocean.cs32x15/results/output.seaice.txt
215 jmc 1.1887 o pkg/atm_phys:
216     - allows to add some damping on uVel,vVel (strength only function of k).
217 jmc 1.1886 o verification, ad-tests:
218     - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
219     global_ocean_ebm and offline_exf_seaice.thsice.
220 dgoldberg 1.1885 o verification/halfpipe_streamice:
221     - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
222     flux input boundary conditions to be ignored; a fix for this bug changed
223 jmc 1.1886 verification results for forward test.
224     - add adjoint test.
225 jmc 1.1884 o pkg/ptracers:
226     - allow to restart without SOM pickup (resetting SOM to zero).
227 m_bates 1.1883 o pkg/gmredi:
228     - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
229     - It uses mixing length theory and suppression by steering level effects to
230     calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
231     to JPO, for more details).
232     - It also uses the diffusivity to calculate an eddy induced streamfunction
233     based on a PV closure (rather than a buoyancy closure as in GM).
234 jmc 1.1884 - New files added to pkg/gmredi:
235 m_bates 1.1883 gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
236     induced overturning streamfunction (called from gmredi_calc_tensor)
237     gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
238     for use in gmredi_k3d
239     gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
240     the eddy diffusivity
241 m_bates 1.1881
242 jmc 1.1880 checkpoint64i (2013/06/18)
243 jmc 1.1879 o pkg/cheapaml:
244     - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
245     that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
246     with pkg/cheapaml.
247     o utils/python: add subpackage for cubed sphere function, first example is
248     simple cs.pcol to plot 2D fields on a map
249 dgoldberg 1.1877 o pkg/streamice:
250     - This is a new package in MITgcm, which solves dynamic equations for ice
251     sheets and ice streams
252 jmc 1.1879 - At the moment it is independent of atmosphere/ocean dynamics, or any
253 dgoldberg 1.1877 other physical packages in MITgcm, even ShelfIce (although it is anticipat-
254     ed that this will change)
255 jmc 1.1879 - There is a new verification exercise that tests it, halfpipe_streamice,
256 dgoldberg 1.1877 evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
257     rectangular embayment
258     - halfpipe_streamice is forward-only for now, will have TAF test soon
259     - for questions, email dgoldber@mit.edu
260 jmc 1.1876 o pkg/thsice:
261     - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
262     of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
263     - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
264     call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
265     - allow precip from pkg/cheapaml to make snow over seaice.
266 jmc 1.1874 o pkg/cfc:
267 jmc 1.1875 - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
268     - remove atmos CFC 2-D arrays from common bloc (now local variables)
269     - change some hard-coded constant to run time parameter for reading and
270     and interpolating atmospheric CFC ; keep same default as previously.
271     - more flexible reading of Atmos CFC (number of records no longer hard-coded)
272     - put arguments in standard order: myTime, myIter, myThid
273     - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
274     atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
275     - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
276     - new routine to print summary of CFC params and check for consistency.
277 mlosch 1.1882 o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
278     similar to thsice_advdiff.
279     Note that for the B-grid case the routine parameters uc/vc are overwritten.
280 jmc 1.1875 o pkg/cfc:
281 jmc 1.1874 - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
282     update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
283 jmc 1.1875 - fix interpolation of atmphspheric CFC between Sorthern and Northern
284     hemisphere value.
285 jmc 1.1873 o pkg/seaice:
286     - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
287 mlosch 1.1872 o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
288     so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
289     - requires an additional time level that is stored in the pickup
290     - you can start with AB2 from a pickup without this time level with
291     pickupStrictlyMatch = .false.
292    
293 jmc 1.1871 checkpoint64h (2013/05/26)
294 jmc 1.1870 o pkg/cheapaml:
295     - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
296     affect machine truncation (but exp cheapAML_box still pass with 13 digits).
297     - consistent treatment of uWind,vWind location: assume everywhere in
298     pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
299     (Note: was already the case for Tair,Qair advection);
300     add option (INCONSISTENT_WIND_LOCATION) to recover old results.
301     - compute diabatic forcing only in the interior (excluding overlap regions)
302     - fill in array "Qsw" (for short-wave heating);
303     - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
304     before any update (consistent with MITgcm state var diagnostics);
305     - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
306     non periodic ; + adjusted for uWind,vWind (C-grid).
307     o pkg/seaice:
308     - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
309     add explicitly pkg/exf in experiments that currently use pkg/seaice.
310     - allows to compile pkg/seaice without pkg/exf.
311 jmc 1.1869 o tools/OAD_support:
312     - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
313     of array "ourStepOf" in function rvNextAction (revolve.F90).
314 jmc 1.1868 o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
315     - change pkg name (to be used with other atmospheric physics pkg)
316     but by-pass CVS when making the new pkg so that we keep the CVS history.
317 jmc 1.1867 o pkg/offline:
318     - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
319     (previously called from pkg/dic_surfforcing_init.F)
320     o model/src:
321     - re-order sequence of calls within packages_init_variables.F, using
322     standard order, except for:
323     DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
324     CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
325 jmc 1.1865 o new pkg: atm_phys
326 jmc 1.1866 - add entry point and source code (previously in contrib
327     verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
328     (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
329 jmc 1.1865 - re-order sequence of calls within packages_readparms.F,
330     packages_init_fixed.F and packages_write_pickup.F
331     (but skip packages_init_variables.F because of TAF issues).
332 jmc 1.1866 - update contrib/*/atm_gray/ experiment.
333 jmc 1.1863 o pkg/seaice (ITD code):
334 jmc 1.1864 - simplify and fix the writing of pickup-files for ITD case
335     o pkg/seaice (ITD code):
336 jmc 1.1863 - introduce floe size dependent lateral melt for ITD case;
337     - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
338     - update seaice_itd experiment main output.
339 jmc 1.1862 o pkg/thsice:
340     - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
341     declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
342     changed accordingly pkg/atm2d.
343    
344 jmc 1.1861 checkpoint64g (2013/05/01)
345 dimitri 1.1859 o pkg/exf ALLOW_RUNOFTEMP
346     - if defined, river and glacier runoff temperature can be read-in from
347     runoftempfile; runoftempfile needs to have same format as runofffile
348 jmc 1.1858 o pkg/thsice (& pkg/bulk_force):
349     - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
350     for energy content of Precip + RunOff & Evap (like with pkg/exf).
351     - change computation domain to always be the interior (without overlap).
352     - fix bug (wrong overlap) when using EXF and stressReduction > 0.
353 jahn 1.1857 o verification/tutorial_global_oce_biogeo:
354     - add preliminary OpenAD setup (still has problems)
355 jmc 1.1861 o pkg/seaice:
356 mlosch 1.1860 - turn some parameters for choosing the convergence criterion of
357     the inexact Newton method (JFNK) into runtime parameters for convenience
358 jmc 1.1861 - clean up seaice_calc_viscosities.F: remove/retire two options for
359 mlosch 1.1860 SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
360     the results of lab_sea/input because a division has been replaced by
361     a multiplication with the reciprocal (sumNorm)
362     - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
363 jmc 1.1861 convergence of solver (changes results, of course), and to test some
364 mlosch 1.1860 new features
365 jmc 1.1856 o model/src:
366     - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
367     - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
368     - move forcing adjustment (balancing surface forcing) in specific S/R
369     where might also be applied exchanges (if needed) to forcing arrays.
370 jmc 1.1855 o pkg/shelfice:
371     - allow to specify the Ice-Shelf mass per unit area (instead of
372     shelficeLoadAnomaly) and do the conversion from one to the other
373     - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
374     to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
375     (b) will be loaded in time (before calling INI_PRESSURE) in case it is
376     needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
377     - update isomip experiment forward output (get machine truncation error
378     from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
379 jmc 1.1854 o verification/offline_exf_seaice:
380     revise data.seaice in input.thermo and input_ad and update results accordingly
381 gforget 1.1853 HO = 0.2, SEAICE_areaLossFormula = 2,
382 jmc 1.1854 SEAICE_growMeltByConv = .TRUE.,
383 gforget 1.1853 SEAICE_doOpenWaterMelt = .TRUE.,
384 jmc 1.1854 Improve consistency with input.thsice and fix the spurious 500m ice corners
385     o verification/global_ocean.cs32x15:
386     - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
387     in icedyn (thsice+seaice-dyn) test and update output.
388     o verification/offline_exf_seaice:
389     - adjust list of tested variables (with testreport) and update
390     standard test output with better slection of monitored fields.
391 jmc 1.1852 o pkg/cd_code:
392     - swtich off Adams-Bashforth on the 1rst iteration. Update output of
393     experiment lab_sea.hb87
394 jmc 1.1851 o tools/genmake2:
395     - change default makedepend from the system default to tools/xmakedepend:
396     When no makedepend is specified, select tools/xmakedepend it the test pass,
397     otherwise select the system default (if exist and pass the test) or
398     try to build cyrus-makedepend ; stop if none of the 3 works.
399 jmc 1.1850 o pkg/exf & pkg/thsice:
400     - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
401 jmc 1.1851 for energy content of Precip + RunOff & Evap. Assumes:
402 jmc 1.1850 1) Rain has same temp as Air.
403     2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
404     3) Run-Off comes at the temp of surface water (with same Cp)
405     4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
406     put directly into Latent Heat flux & should use water-vapor heat capacity.
407     5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
408     with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
409 mlosch 1.1848 o pkg/seaice: simplify the use of CPP flags in JFNK-related files
410     (compile when SEAICE_ALLOW_JFNK is defined)
411 jmc 1.1849 o pkg/thsice:
412     - fix oceanic flux diagnostics & timeave (left from new sequence of calls
413     implementation): move THSICE_AVE call after the advection (called directly
414     from thsice_do_advect.F).
415 heimbach 1.1847 o verification/global_ocean.90x40x15 and OpenAD:
416     New experiment for OpenAD is identical to the one in input_ad except that
417     multiDimAdvection=.FALSE.,
418     There is still an issue with this.
419 jmc 1.1846 o pkg/thsice:
420     - account for ice velocity (ocean relative velocity) in turbulent heat flux
421     at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
422     and offline_exf_seaice (main test).
423    
424 jmc 1.1845 checkpoint64f (2013/03/31)
425     o verification/OpenAD:
426     - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
427     o verification/isomip, pkg/shelfice and OpenAD:
428 heimbach 1.1844 - add OpenAD setup to this exp and make shelfice package work with OpenAD
429 jmc 1.1845 o verification/tutorial_global_oce_biogeo:
430     - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
431     o verification/offline_exf_seaice:
432     - replace adjoint experiment (now similar to fwd input.thermo/ setup).
433 jahn 1.1842 o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
434     - add OpenAD setup to this exp and make ptracers package work with OpenAD
435 jmc 1.1845 o pkg/seaice/seaice_evp.F:
436     mask the asymmetric contribution of the ice-ocean stress (when
437     the turningAngle is non-zero) over open water to avoid stripes
438     in the EVP-solutions after many EVP-substeps. This does not change
439     the verification experiment (because turningAngle=0 in that experiment),
440     but will affect other EVP solutions with turningAngle.ne.0
441 jmc 1.1840 o verification, AD & TLM output:
442     - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
443     additions and multiplications which affect results at machine truncation
444     level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
445     lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
446     (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
447     digits of matching.
448     o pkg/seaice:
449     modify lsr-algorithm so that it vectorizes AND converges by using a
450     "zebra" method: split vector loop into two with step size 2; this
451     solves a general convergence problem for the JFNK solver on a vector
452     computer. It has the potential to even improve convergence for
453     non-vector machines, but it does change the results so it is turned
454     off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
455     SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
456 mlosch 1.1839
457 jmc 1.1838 checkpoint64e (2013/03/05)
458 heimbach 1.1837 o pkg/ecco and several verification experiments:
459 jmc 1.1838 Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
460     from ecco package, and revert to unified routine in model/src/
461     Adjust verification experiments accordingly, especially gloal_oce_llc90
462     Should conclude long-standing work by Gael to reconsile the_main_loop with
463     ECCO and will enable OpenAD's revolve loop in ECCO setup.
464 jmc 1.1835 o pkg/generic_advdiff:
465 jmc 1.1836 - implement compressible flow method for multi-dim advection (similar to
466     gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
467     TAF generates many recomputations) to use it; no yet coded with implicit
468     vertical advection.
469     - change experiment advect_cs (new output) and advect_xy (same output)
470     to test compressible flow multi-dim advection.
471     o pkg/generic_advdiff:
472 jmc 1.1835 - fix SOM advection for unusual cases (linear Free-Surf in r*, other
473     cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
474     o pkg/seaice:
475 mlosch 1.1834 - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
476 jmc 1.1835 bug affects two verification experiments (lab_sea and lab_sea.hb87),
477     recover old (wrong) results by setting noSlipFac = 2. in
478 mlosch 1.1834 seaice_calc_strainrates.F;
479 mlosch 1.1833 - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
480 jmc 1.1835 - add runtime parameter SEAICE_JFNKepsilon for that finite difference
481 mlosch 1.1833 gradient in the Jacobian times vector operation (s/r seaice_jacvec)
482     - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
483 mlosch 1.1831 o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
484     - new subroutines seaice_lsr_tridiagu/v
485     - introduce loop bounds i/jmin/max to be able to use a restricted
486     additive Schwarz method, but not used for now.
487     - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
488     - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
489 heimbach 1.1830 o OpenAD support
490 jmc 1.1838 Reorganize S/R call for overall time-stepping loop to facilitate
491     OpenAD revolve loop replacement
492     (new S/R main_do_loop.F)
493 jmc 1.1829 o model/src:
494     - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
495     - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
496     ADAMS_BASHFORTH2.
497 jmc 1.1828 o pkg/cheapaml:
498     - add new parameter (default=F, same as before) to disable full domain
499     (including land) periodicity in X & Y dir.
500     - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
501     prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
502     into single S/R CHEAPAML_TIMESTEP.
503    
504 jmc 1.1827 checkpoint64d (2013/02/17)
505 jmc 1.1826 o pkg/monitor (angular momentum):
506     - do not add Eta contribution to the total AM if using rigid-lid;
507     - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
508     - horizontal discretisation: compute Zonal wind contribution separately for
509     each component (instead of from cell centered averaged) and use the 4
510     grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
511     - Check that AM is conserved with linear dynamics (momAdvection=F and linear
512     FreeSurf) if using vectorInvariant momentum.
513     o model/src (horizontal grid):
514     - move initialisation of all horizontal grid arrays to null value
515     from specific horizontal grid S/R to main S/R INI_GRID;
516     - add 2 new arrays to project model C-grid velocity on to zonal direction
517     (similar to AngleCosC & -AngleSinC but at U and V point location) and
518     compute them in S/R CALC_GRID_ANGLES.
519 mlosch 1.1825 o pkg/seaice: replace a hard coded parameter by a runtime parameter
520 jmc 1.1826 SEAICE_JFNK_tolIter
521 mlosch 1.1824 o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
522     preconditioner for JFNK (run LSR into the overlaps as far as possible,
523     i.e OLx/y-2, but overwrite the solution in the overlaps)
524     - extend loop range in seaice_calc_viscosity
525     - add new parameters SEAICE_OLx/y (default = OLx/y-2)
526     - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
527     - slightly modify loops in tridiagonal solver lsr-preconditioner
528     - by default remove the extra exchange in seaice_preconditioner with a
529     replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
530     - modify offline_exf_seaice so that old results without RAS are reproduced
531     for output.dyn_jfnk.txt
532     in seaice_fgmres.F (unrelated to RAS)
533     - add a cpp-flag option for a re-ordered mapping (potentially more
534     efficient), but because this changes the results, turn it off by
535     default
536     - replace the save statement by local common blocks
537 jmc 1.1823 o utils/matlab:
538     - fix tile-offset in rdmnc.m when output was produced using EXCH2.
539     - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
540     instead of local script "load_cs.m".
541 mlosch 1.1822 o pkg/seaice:
542     - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
543     to the scalarProductMetric and the unrolling. By chance this does not
544 jmc 1.1823 change the verification experiment, because of the particular domain
545 mlosch 1.1822 decomposition
546 jmc 1.1820 o pkg/diagnostics:
547     - change default missing_value from UNSET_RL to -999.
548 mlosch 1.1821 o pkg/layers: improve vectorization of layers_fluxcalc.F
549 jmc 1.1823 - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
550 mlosch 1.1821 time spent in this routine by more than a factor of 3 on an NEC-SX8
551     - step 2: replace search algorithm by a bisection algorithm found in
552 jmc 1.1823 Press et al. Numerical Recipes in Fortran. This algorithm can be
553 mlosch 1.1821 vectorized and finds the correct bin in approx. log2(Nlayers) steps.
554     For now, use this algorithm only for TARGET_NEC_SX defined.
555     - moved the search algorithm into a separate subroutine, that is kept
556     within the same file for automatic inlining.
557     - modified catching potential errors
558 jmc 1.1820 o pkg/ecco:
559 gforget 1.1818 - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
560 jmc 1.1820 o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
561 gforget 1.1818 - modifications for ALLOW_GENTIM2D_CONTROL
562     -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
563     -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
564     -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
565     -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
566 jmc 1.1816 o model/src:
567     - account for moist thermodynamics in (dry) potential temperature equation;
568     update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
569     and cpl_aim+ocn.
570 jmc 1.1817 - also switch to standard compiler (gfortran, was using ifort previously)
571     for fizhi-cs experiments reference output.
572 jmc 1.1816 o pkg/ctrl:
573 heimbach 1.1815 - 1st step toward generic time-varying control variable (2D) via CPP option
574     ALLOW_GENTIM2D_CONTROL
575     - note new namelist ctrl_nml_genarr in data.ctrl
576 jmc 1.1814 o verification/global_ocean.cs32x15:
577     - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
578     thsice calling sequence and update "output.icedyn.txt" output file.
579 jmc 1.1813 o pkg/ptracers:
580     - from Ryan A.: code to allow to restart a tracer at regular time interval
581     specifying a reset frequency and a reset-phase (for each tracers).
582 jmc 1.1811 o pkg/thsice:
583 jmc 1.1812 - implement new sequence of calls for thsice+seaice:
584     previously: ice-Dyn,ice-Advect,ice-Thermo(thsice)
585     new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
586     - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
587     in CPP_OPTIONS.h) to recover old sequence;
588     - update diagnostics for Intermediate State thsice diagnostics: now filled
589     just before advection (instead of just after advection in old sequence);
590     - update output of experiment offline_exf_seaice (standard test);
591     - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
592     by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
593     o pkg/aim_v23:
594     - use tiled array for aim_CO2 and surface wind speed for export to coupler;
595     - use standard pkg/mdsio routines to read & write CO2 pickup file;
596     - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
597     - Implement new sequence of calls for seaice advection (with thsice and
598     seaice diffusion): do ice advection after ice-Thermodynamic (previously
599     was done before); change aim_do_physics.F (split the bi,bj loops block);
600     - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
601     o pkg/thsice:
602 jmc 1.1811 - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
603     where just seaice diffusion is used without seaice-dynamics.
604    
605 jmc 1.1810 checkpoint64c (2013/01/18)
606     o pkg/seaice:
607     - add a parameter JFNKres_tFac that can replace JFNKres_t
608 mlosch 1.1809 (= JFNKres_tFac*JFNKresidual before JFNK solver)
609     - add a line search option to the JFNK solver
610 jmc 1.1810 - move update of u/vIce and computation of initial residual into a separate
611 mlosch 1.1808 routine (same file); makes the code a little easier to read (?)
612     - the line search requires computation of the residual and for some reason
613 jmc 1.1810 I cannot do the update of u/vIce at the beginning of the Newton loop
614 mlosch 1.1808 without changing the results, so we move computation of the new residual
615     also to the end of the Newton loop, even without the line search
616 jmc 1.1806 o pkg/mdsio:
617     - write missing value (corresponding to undefined array value) to meta files;
618 jmc 1.1810 skip this if missing value is one (UNSET_RL would be a better value for the
619 jmc 1.1806 case of undefined missing value but it's current the default missing-value);
620     Also update mdsio_read_meta.F (reading timeInterval & missing-value).
621 jmc 1.1805 o pkg/exf & thsice:
622 jmc 1.1810 - for diagnostics purpose, fill-up and update Qsw array (+ fill the
623 mlosch 1.1809 diagnostics) even when SHORTWAVE_HEATING is #undef;
624 jmc 1.1805 o verification/cfc_example:
625 jmc 1.1810 - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
626 mlosch 1.1809 illustrate how to use it).
627 jmc 1.1804 o verification/offline_exf_seaice:
628     in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
629     files to only one time-record.
630     in input.thermo: narrow the 2 bands of low initial ice-concentration near
631     N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
632 jmc 1.1810 snapshot output; same mcPheePiston value as in thsice with
633 mlosch 1.1809 surf-current=0.2m/s.
634 jmc 1.1804 in input.thsice: similar set-up as in input.thermo (channel with same seaice
635     initial conditions).
636 jmc 1.1803 o verification/cfc_example:
637     - update file "data" with more standard choice (default rotationPeriod,
638     exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
639     set deltaTFreeSurf to deltaTtracer) and update the output.
640     o pkg/layers:
641     - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
642     - ensure that "layers_bolus" is switched to False when useGMRedi=False.
643     o verification/offline_exf_seaice:
644     - set all {field}period to zero for constant-in-time forcing (not tested
645     anywhere else).
646 jmc 1.1802 o verification/offline_exf_seaice:
647     - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
648     - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
649 jmc 1.1801 o model/src:
650     - implement Finite-Volume method for (hydrostatic) presure gradient
651     from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
652     o pkg/seaice: implement EVP* by Lemieux et al. (2012).
653     - In order to be compatible with the default EVP code, this requires changing
654     the EVP code around a little; and because any small change immediately
655     breaks the lab_sea.hb87 verification experiment, the reference output is
656     updated two times (each time the remaining aggrement was only 2 digits):
657     - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
658     - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
659     The adjoint test lab_sea.evp also needed to be updated.
660     - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
661     SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
662     a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
663     explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
664     INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
665     kept obscure, because I need to test it a little more.
666 jmc 1.1799 o pkg/cheapaml:
667     - fix few incorrect type (_RL/_RS) in subroutine calls.
668     o pkg/seaice:
669     - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
670     to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
671 jmc 1.1798 o model/src:
672     - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
673     change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
674     experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
675 jmc 1.1796 o pkg/cheapaml:
676     - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
677     update output of experiment cheapAML_box.
678 jmc 1.1797 - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
679     and set them only in one place (cheapaml_readparms.F).
680     - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
681     - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
682     and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
683 gforget 1.1795 o model/src/the_main_loop.F:
684     - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
685     o pkg/seaice:
686     - remove legacy branch code.
687     - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
688     o verification/*/code*/SEAICE_OPTIONS.h:
689 jmc 1.1797 - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
690 jmc 1.1796 SEAICE_CAP_HEFF).
691 jmc 1.1794 o pkg/cheapaml:
692     - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
693     to load new forcing fields.
694     - add missing "_d 0" where it's needed; + some editing (improve indentation).
695     - remove switch to "-r8" compiler option (no longer needed) in verification
696     cheapAML_box, keep same output (small trucation error differences).
697 jmc 1.1793 o verification/offline_exf_seaice:
698 gforget 1.1792 - add thermodynamics only test.
699 jmc 1.1793 o verification/cheapAML_box:
700     - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
701     keep same output (same 14 digits for cg2d).
702     - switch on "-r8" compiler option (some numerical values are missing
703     the "_d 0") and update output (only 6 digits for cg2d were preserved).
704 gforget 1.1792
705 jmc 1.1791 checkpoint64b (2012/12/24)
706 jmc 1.1790 o pkg/cheapaml:
707     - remove un-used variables (Qnet,EmPmR) from pickup files.
708     - store tendency of advected variables into cheapaml pickup file
709     and fix the AB-2 restart.
710 gforget 1.1789 o verification/offline_exf_seaice and lab_sea adjoint:
711 jmc 1.1790 - switch to new code (#undef SEAICE_GROWTH_LEGACY).
712     - switch to 4 time steps in offline, consistent with lab_sea.
713 jmc 1.1791 - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
714 jmc 1.1790 - update results after change of experiment seaice.
715 jmc 1.1791 o pkg/seaice:
716     - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
717     parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
718     still defined since SEAICE_multDim needs to be set to MULTDIM value (from
719     SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
720 jmc 1.1788 o model/src:
721     - add run-time parameter to select CG2D solver minimum-residual solution
722     (in case of a poor convergence).
723 mlosch 1.1786 o pkg/seaice/seaice_lsr.F
724 jmc 1.1788 - move calculation of matrix coefficients into new
725 mlosch 1.1787 S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
726     file; the main purpose of this change is to be able to reuse the code
727     in S/R SEAICE_PRECONDITIONER
728 mlosch 1.1786 - modify the computation of the residual so that the mass of sea-ice
729 jmc 1.1791 is not used twice; this simplifies the calculations, but since
730 mlosch 1.1786 the residual is never used except when LSR_mixIniGuess.ge.4---and this is
731     not tested in testreport---this does not affect the testreport results.
732 dimitri 1.1785 o verification/seaice_obcs:
733     - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
734     verification/lab_sea/input.salt_plume; changes results/output.txt*
735 jmc 1.1784 o model/src:
736     - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
737 mlosch 1.1783 o pkg/seaice:
738     - improve description of parameters in seaice_fgmres.F and start
739     cleaning up the code
740 jmc 1.1784 - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
741 mlosch 1.1783 second argument
742     - add a metric based on grid cell area to SEAICE_SCALPROD; update
743     results of offline_exf_seaice.dyn_jfnk
744     - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
745 jmc 1.1782 o pkg/aim_v23:
746     - fix an other bug in dissipation heating (grid-cell area was missing).
747 jmc 1.1781 o model/src + pkg/seaice:
748     - add global (multi-tile) linear solver for pair of tri-diagonal system
749     along X and Y lines, respectively for U and V component.
750     Note: 1) MPI and cube-exchange not yet coded.
751     2) probably not accurate for poorly conditioned / large size problem.
752     - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
753     default: not compiled and not used.
754 mlosch 1.1780 o pkg/seaice:
755     - first attempt at a multi-threaded fgmres solver for the JFNK solver:
756 jmc 1.1781 introduce bi/bj loops and use global_sum_tile_rl instead of
757 mlosch 1.1780 mpi_allreduce in seaice_fgmres.F
758     - improve diagnostics output for fgmres solver (seaice_fgmres.F)
759     - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
760     - add a verification experiment for JFNK in offline_exf_seaice
761 jmc 1.1778 o verification:
762 jmc 1.1779 - change (for now, only fwd test) offline_exf_seaice experiment:
763 jmc 1.1791 use a re-entrant channel with idealized coastline (trapezoidal shape)
764 jmc 1.1779 at southern boundary to explore seaice dynamics and thermodynamics
765     with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
766     secondary test (input.thsice) use thermodynamics only with SST relaxation.
767     - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
768     o pkg/exf:
769     - disable "sstExtrapol" when Nr=1
770     o verification:
771 jmc 1.1778 - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
772     to test pkg/cheapaml.
773 jmc 1.1777 o pkg/aim_v23 & pkg/shap_filt:
774     - fix dissipation heating (erroneous gravity multiplication factor).
775     o pkg/seaice:
776 mlosch 1.1776 - remove unused field pressPre from jfnk solver
777     - rename two subroutines in seaice_preconditioner.F
778 jmc 1.1775 o eesupp/src:
779     - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
780 mlosch 1.1774 o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
781     - remove wrong parts of the rhs and the lhs (were in there
782     because I did not understand the concept of this preconditioner)
783     - add an exchange between u- and v-sweep. This increases communication
784     by a factor of two but improves the convergence of jfnk. Ideally,
785     one would like the u- and v-sweep to be independent. So far within
786     undocumented ifdefs
787     - reorganize the extra computations for printing the residuals
788 jmc 1.1773 o tools/genmake2:
789     - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
790     since it's not necessary (and was preventing to use MNC in some cases).
791    
792 jmc 1.1772 checkpoint64a (2012/11/16)
793 jmc 1.1771 o pkg/autodiff:
794     - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
795     autodiff_readparms.F no longer depends on calling order (within
796     packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
797     rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
798     and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
799 dimitri 1.1770 o pkg/obcs:
800     - adding tidal velocity forcing capability to obcs
801     for usage example, see verification/seaice_obcs/input.tides
802 mlosch 1.1768 o pkg/seaice:
803 jmc 1.1771 - turn the LSR-relaxation parameters WFAU/V into runtime parameters
804 mlosch 1.1768 SEAICE_LSRrelaxU/V
805 mlosch 1.1769 - introduce runtime parameter SEAICEetaZmethod (=0 by default)
806 jmc 1.1767 o pkg/aim_v23:
807     - implement heating from friction (bottom friction and stratospheric drag).
808     o pkg/shap_filt:
809     - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
810     dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
811 jmc 1.1766 o model/src:
812     - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
813     time-constant addMass field from file (addMassFile);
814     - support for heating due to friction (and Kinetic Energy dissipation):
815     add option, run-time switch and 3-D field array + support code ; each pkg
816     or S/R can add heating contribution (if there is a sink of KE); the sum is
817     accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
818 mlosch 1.1761 o pkg/seaice:
819 heimbach 1.1765 - complete merge of ITD code into seaice_growth.F
820     from MITgcm_contrib/torge/itd/code/
821     no verification so far, but Torge Martin tested
822     "1-D test case and Beaufort set up;
823     deliver okay results after 1 model year."
824     - complete merge of SEAICE_SIZE.h into all relevant routines
825 mlosch 1.1764 - move computation of eta at Z-points into calc_viscosities
826     + introduce global field etaZ
827     + add different methods for computing etaZ, for now the old
828     method (simple averages of eta to Z-points) is hardwired
829 jmc 1.1766 + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
830 mlosch 1.1764 seaice_preconditioner
831     - simplify computations for SEAICE_ZETA_SMOOTHREG
832 jmc 1.1766 - seaice_preconditioner:
833 mlosch 1.1763 + replace one remaining press by pressLoc (mistake)
834     + adjust printing of residuals
835 mlosch 1.1762 - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
836 jmc 1.1766 + add (SEAICE.h) and rename some counters (initiliased in
837 mlosch 1.1762 seaice_init_fixed.F)
838     + add _BEGIN/END_MASTER (myThid) around print statements
839     + print total number of iterations and failures over SEAICE_monFreq
840     interval to STDOUT
841     - move control over output-messages by fgmres to seaice_jfnk to save
842     some operations
843 mlosch 1.1761 - move resetting initial guess for fgmres outside of seaice_fgmres_driver
844     in order to make restarts with sol .ne. zero (fgmres with restarts)
845     (seaice_jfnk.F, seaice_fgmres.F)
846     - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
847     a serious convergence problem when open boundaries are involved
848 jmc 1.1766 o pkg/ggl90: fix computation of control volumes for the case of
849 mlosch 1.1759 ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
850     up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
851 mlosch 1.1758 o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
852 heimbach 1.1757 o pkg/autodiff
853     - Add inAdMode switch for SEAICEuseDYNAMICS:
854 jmc 1.1766 SEAICEuseDYNAMICSinAdMode
855 heimbach 1.1757 (extend logic in ADAUTODIFF_INADMODE_SET)
856 heimbach 1.1756 o pkg/seaice
857     - Step 1 of merging ice-thickness distribution (ITD) code from
858     MITgcm_contrib/torge/itd/ (author: Torge Martin)
859     The code implements concept laid out in Thorndike et al. (1975);
860     code is enabled via CPP flag SEAICE_ITD
861     nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
862     code is not complete yet!!
863 heimbach 1.1757 - SEAICE_SIZE.h now included in almost all seaice routines
864 jmc 1.1755 o verification (using seaice):
865     - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
866     global_ocean.cs32x15.seaice ; update results.
867     - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
868     - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
869     offline_exf_seaice (previously compiling B-grid).
870 jmc 1.1754 o pkg/exf:
871     - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
872     to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
873     forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
874 jmc 1.1751 o pkg/layers (adjust changes from Sept 19):
875 jmc 1.1752 - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
876     this allows to remove "layers_maxNum" dimension from all layers arrays.
877     o pkg/layers (adjust changes from Sept 19):
878 jmc 1.1751 - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
879     - snap-shot extended to all type of layers (not just the 1rst type);
880     - remove layers variables when corresponding CPP option is undef.
881     o pkg/layers:
882     - rename pkg/layers variable and add new output (layer exist & un-weighted
883     velocity in layer)
884     o pkg/seaice:
885 mlosch 1.1750 - simplify (?) ocean-drag coefficent computations by using
886     the same routine in all three solvers (saves some code lines)
887     - remove global fields DRAGA and DRAGS from C-grid code and
888     declare them locally in lsr.F (the only place where they are
889     still used)
890 jmc 1.1753 - update AD output of lab_sea.evp (very sensitive anyway).
891 mlosch 1.1749 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
892     (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
893     and SEAICEuseJFNK=.true. A few things to note:
894     - involves a FGMRES, that is parallel but very inefficient,
895     because of many scalar products (global sums) in the Gram-Schmidt
896     orthogonalization method. Needs to be replaced. Original code
897     from J.-F. Lemieux
898     - preconditioner for FGMRES is a stripped down version of LSOR
899 jmc 1.1751 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
900 mlosch 1.1749 preconditioner. For the preconditioner, the default is set to 10.
901     - Jacobian times vector is computed with finite differences
902     - marginally related to JFNK-solver: add a smooth regularization for
903     zeta with tanh that will improve convergence (Lemieux and Tremblay,
904     2009) for any implicit solver (not implemented for EVP because EVP
905     does not need this regularization in the first place). Define
906     SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
907 jmc 1.1748 o eesupp/src:
908     - check in genmake2 that intrinsic S/R flush is available.
909     - add S/R to flush IO unit (if intrinsic S/R flush is available)
910     - flush standard & error msg unit before MPI termination
911     - if debugMode, flush IO unit after printing msg
912     o pkg/ctrl:
913     - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
914     to ctrl_set_unpack_xyz.
915    
916 jmc 1.1747 checkpoint64 (2012/10/09)
917 heimbach 1.1745 o pkg/shelfice
918 jmc 1.1747 - in mom_fluxform.F, mom_vecinv.F:
919     CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
920     Bug fix KappaRU -> KappaRV
921     does not change verification/isomip but may change other setups
922     (presumably constant KappaRU=KappaRV)
923 mlosch 1.1746 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
924 dimitri 1.1744 o pkg/obcs:
925     - fixed some indexing bugs in obcs_seaice_sponge.F
926     - added obcs relaxation subroutines for HSALT and HSNOW
927     - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
928 mlosch 1.1743 o pkg/seaice:
929     - add "multicategory" parameterization for snow in analogy to ice,
930     default is off for now.
931 jmc 1.1741 o pkg/obcs:
932 dimitri 1.1742 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
933     see verification/seaice_obcs/input.seaiceSponge for example application.
934 jmc 1.1741 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
935     index setting by master-thread. This fix multi-threads Pb in previous modifs.
936 gforget 1.1740 o pkg/layers :
937 jmc 1.1741 - add diagnostics to pkg/layers
938     - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
939     (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
940 gforget 1.1740 o pkg/generic_advdiff/gad_implicit_r.F :
941 jmc 1.1741 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
942     o pkg/seaice/seaice_growth.F:
943 gforget 1.1740 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
944 jmc 1.1738 o pkg/obcs:
945 jmc 1.1739 - change default setting of OBCS_UVICE_OLD from defined to undef;
946     - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
947     in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
948     - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
949     - change OB null index value (OB_indexNone) to -99 ; this fix the problem
950     with Southern & Western OB at a tile edge (at least in a simple set-up).
951     o pkg/obcs:
952 jmc 1.1738 - change settings of OB index in case OB coincides with tile edge (shared by
953     2 tiles), so that common OB location is registered by both tiles (instead of
954     only 1). However, for Southern and Western OB, index value = 0 is not
955     recognized as valid OB index (=default null value) and needs to be fixed.
956     - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
957 jmc 1.1739 - new parameter "OB_indexNone" for null index value (for now, still zero)
958 jmc 1.1738 to replace hard-coded null index value of zero.
959 jmc 1.1737 o pkg/exch2:
960     - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
961     always check buffer-size (but outside the loop); move checking for valid
962     index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
963     print each tile and point connection only if |W2_printMsg|>= 2 and 3.
964 jmc 1.1736 o pkg/ctrl (pack & unpack):
965     - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
966     (locally defined) for different variables (+ remove the variable-specific
967     file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
968     (to be extended to other local file names in ctrl.h).
969     o pkg/flt:
970     - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
971 jmc 1.1735 o pkg/mdsio:
972     - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
973 jmc 1.1734 o tools/genmake2:
974     - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
975     (added by Alistair in version 1.51 for building without make depend);
976     - remove Header files list (H_SRC_FILES) from the dependence of targets
977     ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
978     place in version 1.23): this save going through staf when unrelated header
979     file has been modified.
980     Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
981     "make depend" step, still need to do "make links" before "make adtaf".
982 jmc 1.1733 o eesupp/src (+ few pkg src files) & genmake2:
983     - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
984     - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
985 jmc 1.1734 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
986 jmc 1.1733 upper/lower case ; account for space between "#" and undef/define)
987     o pkg/flt (with exch2):
988     - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
989 jmc 1.1734 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
990 jmc 1.1733
991 jmc 1.1730 checkpoint63s (2012/09/05)
992 gforget 1.1731 o pkg/ecco:
993 jmc 1.1732 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
994     - add more relevant #ifdef ALLOW_SMOOTH ones.
995     - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
996 gforget 1.1731 o pkg/ctrl:
997     - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
998     ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
999 jmc 1.1732 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
1000     doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
1001     ctrlSmoothCorrel3D (new).
1002 gforget 1.1731 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
1003     - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
1004 jmc 1.1732 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
1005 gforget 1.1731 controls when useAtmWind, and vice versa.
1006     - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
1007     - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
1008 jmc 1.1732 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
1009     - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
1010     #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
1011     - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
1012     replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
1013 gforget 1.1731 o pkg/smooth:
1014 jmc 1.1732 - remove un-necessary includes.
1015     - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
1016     Those CPP options were never defined, and not necessary.
1017 gforget 1.1731 o model/src:
1018     - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
1019     - standard treatment of useSMOOTH.
1020     o pkg/autodiff:
1021 jmc 1.1732 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
1022     useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
1023 jmc 1.1729 o pkg/exch2:
1024     - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
1025 gforget 1.1731 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
1026 jmc 1.1729 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
1027     and tiles to process mapping.
1028     - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
1029     moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
1030     rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
1031     from w2_eeboot.F to w2_readparms.F.
1032     o eesupp/src:
1033     - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
1034     ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
1035     also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
1036     - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
1037     is defined (remove condition on usingMPI) to match cases where MPI_INIT
1038     has been called.
1039     - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
1040     - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
1041     (so that on 1 proc, get same myPid independently of usingMPI)
1042     - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
1043     useCubedSphereExchange with EXCH-1 (safer).
1044     - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
1045 jmc 1.1728 o pkg/ggl90:
1046     - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
1047     used in ALLOW_GGL90_SMOOTH code.
1048     o pkg/flt:
1049     - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
1050     floats at the Southern end of the domain).
1051     o eesupp/inc:
1052     - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
1053     but not used (and not to be used) anywhere, just for documentation.
1054 jmc 1.1727 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
1055     - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
1056     a) can damage previously written records in any other multi-record files.
1057     b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
1058 jmc 1.1726 o tools/genmake2:
1059     - define variable MAKE within Makefile and use it in place of 'make';
1060     - update AD_CONFIG.h (if needed) before building any of the executable
1061     (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
1062     and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
1063     - always print usual warning comment 'this file is automatically generated'
1064     from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
1065 jmc 1.1727 o pkg/cheapaml:
1066     - updated to correspond to the code used in accepted paper (Nico Wienders).
1067 jmc 1.1726 o pkg/exf:
1068     added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
1069     ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
1070     and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
1071     o pkg/exf, autodiff, ctrl, ecco and seaice:
1072     remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
1073     o pkg/ctrl, ecco:
1074     allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
1075     Depending on useAtmWind, one is inactive, and the other is active (see
1076     exf_getffields.F/exf_getsurfacefluxes.F).
1077 jmc 1.1724 o tools/genmake2:
1078     - improve error msg when failing in 2nd test of check_for_broken_Ff
1079     - fix option '-makefile' short-name (-mf according to genmake2 -help)
1080     - source local config file "genmake_local" just after processing the genmake2
1081     command arguments (previously done before processing arg).
1082 jmc 1.1723 o pkg/grdchk:
1083     - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
1084     to this routine from cost_final has been dropped in g_cost_final)
1085     - improve printed information (more explicit msg, no longer using "print *,"
1086     fix fcpertminus printed value).
1087 jmc 1.1722 o model/src:
1088     - move call to COST_INIT_VARIA out of packages_init_variables.F directly
1089     into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
1090     this prevents getting cost-funct reset in adinitialise_varia recomputations.
1091 jmc 1.1721 o pkg/dic:
1092     - move initialisation of "freefe" array from from dic_biotic_forcing.F to
1093     fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
1094     o pkg/grdchk:
1095 gforget 1.1720 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
1096 jmc 1.1721 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
1097 gforget 1.1719 o pkg/autodiff/ctrl/grdchk :
1098 jmc 1.1721 - attempt to sort out what works and what does not,
1099 gforget 1.1719 with regard to I/O, and to warn/stop accordingly.
1100 jmc 1.1721 o pkg/grdchk:
1101 gforget 1.1719 - attempt to fix grdchk in the case of useSingleCpuIO.
1102     - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
1103     statements were moved from grdchk_main.F and into
1104     grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
1105     - a global sum is applied to record numbers icvrec/layer
1106     out of grdchk_loc so that they be passed to I/O routines.
1107 jmc 1.1721 o pkg/smooth:
1108     - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
1109 gforget 1.1719 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
1110 jmc 1.1717 o verification/testreport:
1111     - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
1112     - can also use compressed (gzip) reference output file;
1113     - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
1114     to be easier to collect by testreport.
1115     - update existing TLM output (half out-of-date by more than 3 yrs).
1116 jmc 1.1718 - report NETCDF & LAPACK settings (from genmake2) in output dir.
1117     - report run-time in each individual summary (previously only for AD test);
1118     for TLM test, add also TAF version.
1119     - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
1120 jmc 1.1717
1121 jmc 1.1716 checkpoint63r (2012/08/15)
1122     o tools/genmake2:
1123     - fix Makefile for target ftlall (+ update files to clean after make ftlall)
1124 gforget 1.1715 o pkg/ecco/ecco_cost_final.F :
1125 jmc 1.1716 - fix fc print statements (to stdout and costfunction0000) so
1126 gforget 1.1715 that the printed value is always after the global sum.
1127     o pkg/seaice/seaice_dynsolver.F :
1128     - fix ice strength assymptote at SEAICE_area_max<1
1129     (no change for the standard case of SEAICE_area_max=1)
1130 jmc 1.1714 o some cleaning:
1131 jmc 1.1716 - pkg source files: ensure that all *.F files from each pkg included the
1132 jmc 1.1714 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
1133 jmc 1.1716 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
1134 jmc 1.1714 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
1135 jmc 1.1716 includes;
1136 jmc 1.1714 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
1137 jmc 1.1716 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
1138     is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
1139 jmc 1.1714 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
1140     - update option-file CPP_OPTIONS.h of all AD experiments:
1141 jmc 1.1716 * no longer include PACKAGES_CONFIG.h ;
1142     * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
1143     * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
1144 jmc 1.1714 including ECCO_CPPOPTIONS.h).
1145 jmc 1.1713 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
1146     - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
1147     separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
1148     not necessary accurate).
1149     - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
1150     pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
1151     deliberately break compilation (a remainder that it needs to be customized)
1152     - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
1153     - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
1154     - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
1155     o tools/genamke2:
1156     - check for lapack.
1157 gforget 1.1712 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
1158 jmc 1.1713 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
1159     jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
1160     from both packages.
1161 gforget 1.1712 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
1162     - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
1163 jmc 1.1713 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
1164     of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
1165 gforget 1.1712 o pkg/cost : add comments to explain special and/or untested setups.
1166 jmc 1.1711 o pkg/exf:
1167     - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
1168     (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
1169     o verification/*/code_ad:
1170     mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
1171     - reccord when this file is included (define ECCO_CPPOPTIONS_H)
1172     - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
1173     allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
1174 gforget 1.1710 o pkg/seaice :
1175 jmc 1.1711 - added possibility to change ice strength/PRESS0 relationship to
1176     HEFF, according to the following run time parameters
1177     SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
1178     SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
1179     SEAICEpresH0 :: HEFF threshold for ice strength (m)
1180 gforget 1.1710 o pkg/ggl90 :
1181 jmc 1.1711 - added run time flag mxlSurfFlag to include the code that ensure
1182 gforget 1.1710 mixing between first and second level (previously included as a comment)
1183 gforget 1.1709 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
1184 jmc 1.1711 - add test of newly added dumpAdByRec=T option where
1185 gforget 1.1709 we write all records to one file per variable.
1186     o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
1187     - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
1188     to check that this code is ok with taf and compiles in adjoint.
1189     o pkg/autodiff :
1190     - added run time param dumpAdByRec : ad dump format switch.
1191 jmc 1.1711 If true then write all records to one file per variable.
1192     Else write one file per record (remains the default).
1193 gforget 1.1709 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
1194 gforget 1.1708 o pkg/seaice:
1195     - Added SEAICEuseTILT run time switch : if set to
1196 jmc 1.1711 false then omit the tilt term in seaice dynamics.
1197 gforget 1.1708 - Fix free drift calculation.
1198 heimbach 1.1707 o pkg/shelfice:
1199 jmc 1.1711 When initializing SHELFICEDragQuadratic, set default to be
1200     consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
1201 heimbach 1.1707 but retain option to set it independently
1202     (inconsistenty spotted by Veronique Dansereau)
1203 jmc 1.1706 o eesupp/inc:
1204     - in EEPARAMS.h, add real-type constant for some frequently used simple number
1205     (0,1,2,1/2), with name explicitly referring to RS/RL type.
1206     o model/src:
1207     - move balancing of relaxation terms to new S/R balance_relax.F.
1208 jmc 1.1702 o pkg/autodiff:
1209     re-write active I/O high-level (control) S/R:
1210     - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
1211     - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
1212     - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
1213     MDS_READ/WRITE_FIELD); change loops to multi-threads.
1214     - update and merge active_file_control_slice.flow into active_file_control.flow
1215     - update the calls in lower level S/R (active_file.F, active_file_g.F and
1216     active_file_ad.F) keeping the argument list and function unchanged.
1217 jmc 1.1703 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
1218     =.TRUE.") and remove high-level (control) _loc version (not called anymore).
1219 jmc 1.1704 - new low-level active I/O routines, one for each type (RL/RS), for active var
1220     of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
1221     fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
1222     right type.
1223 jmc 1.1702 o autodiff and RS=real*4:
1224     - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
1225     ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
1226     - change argument type of 3-D mask argument to _RS to match type in the call
1227     (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
1228 jmc 1.1701 o pkg/thsice:
1229     - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
1230     - option to correct ocean fresh-water flux for imbalance of Atmos+Land
1231     fresh-water flux: uniform correction or proportional to local precip.
1232 heimbach 1.1700 o pkg/ctrl:
1233     - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
1234     - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
1235     ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
1236     - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
1237 jmc 1.1701
1238 jmc 1.1699 checkpoint63q (2012/07/30)
1239 jmc 1.1697 o pkg/autodiff:
1240     note about monitor and snap-shot of ad-variables:
1241     a) need to apply ADEXCH before monitor or output of ad-vars to include
1242     overlap contributions (was done for adjDump but missing for monitor).
1243     b) since ADEXCH implies adding overlap values to interior array, machine
1244     truncation error is expected when adding an ADEXCH call in the middle of
1245     the time-stepping (although mathematically identical).
1246     modifs:
1247 jmc 1.1698 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
1248     declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
1249 jmc 1.1697 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
1250     apply ADEXCH before monitor or snap-shot of ad-variables:
1251     =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
1252     - implement new method (copy+adexch) for snap-shot and monitor of main model
1253 jmc 1.1698 ad-vars (initially not used by default -> output unchanged).
1254     - change default (set to 2) to use new method and update few output_adm.txt
1255     with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
1256     and both tutorial_tracer_adjsens tests).
1257     - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
1258     and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
1259 heimbach 1.1696 o pkg/ctrl:
1260     enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
1261     generic control variables via
1262     #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
1263     Only required customization should be S/R ctrl_map_ini_genarr.F
1264     (routine in repository contains example)
1265 jmc 1.1695 o pkg/exf:
1266     - fix and refine checking of surface-relaxation setting when using EXF
1267 jmc 1.1694 o verification (adjoint exp):
1268     - reduce length of simulation by half for experiment global_ocean.cs32x15
1269     (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
1270 mlosch 1.1693 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
1271 jmc 1.1694 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
1272 mlosch 1.1693 of KE that can occur with aggressive optimization
1273 jmc 1.1694 + put quadratic bottom drag calculation in separated loops (only done if
1274     using bottomDragQuadratic)
1275 jmc 1.1692 o model/src: CG2D_NSA
1276     - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
1277     and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
1278     - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
1279     change cg2d residual target to be expressed in Wunits (=> do not normalise
1280     RHS ; this fix global_max Pb with TAF); update output.
1281 jmc 1.1691 o verification/tutorial_tracer_adjsens:
1282 jmc 1.1692 improve parameter consistency (and get rid of warnings):
1283 jmc 1.1691 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
1284     - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
1285     - use staggerTimeStep (for stability) in som81; use default rotation period.
1286 jmc 1.1690 o pkg/exch2:
1287     - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
1288     reset to 0 = 1 long line in X)
1289     o pkg/mdsio:
1290     - fix reading of dimensions from meta file for large-size domain
1291 jmc 1.1689 o model/src:
1292     - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
1293     - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
1294     Cubed-Sphere Exch with CS-corners inside the domain;
1295     make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
1296     globalArea and to set hasWetCSCorners.
1297     - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
1298     metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
1299     - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
1300     useCDscheme and useCubedSphereExchange).
1301 gforget 1.1688 o pkg/seaice/seaice_growth.F :
1302 jmc 1.1689 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
1303     for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
1304     when the previous code was not correct.
1305     - in all cases diagnoze the boundary condition mismatch to SIaaflux
1306     - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
1307     that term to QNET (essentially to set the melt/freeze water to 0degC).
1308     when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
1309 gforget 1.1687 o verification/global_ocean.cs32x15/input.seaice :
1310 jmc 1.1689 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
1311     - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
1312     - update results (output.seaice.txt) accordingly.
1313 gforget 1.1687 o verification/lab_sea/input/data.seaice :
1314 jmc 1.1689 - remove SEAICEheatConsFix, which is now be tested
1315     in global_ocean.cs32x15. The presently coded fix
1316     is only consistent with real fresh water + nlfs.
1317     - update results (output.txt) accordingly.
1318 gforget 1.1686 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
1319 jmc 1.1685 o AD_CONFIG.h file:
1320 jmc 1.1689 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
1321     - remove #include "AD_CONFIG.h" from all included OPTIONS files and
1322     add it explicitly in each fortran src file where it is needed.
1323     motivation: header file AD_CONFIG.h is generated/modified after "make depend"
1324     thus introducing potentially wrong dependency; therefore, better to include
1325     it only where it's really needed, and after any other included OPTIONS file
1326     (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
1327     or ALLOW_TANGENTLINEAR_RUN).
1328 jmc 1.1685
1329 jmc 1.1684 checkpoint63p (2012/07/06)
1330 jmc 1.1681 o pkg/autodiff:
1331     - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
1332     - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
1333     which are now read from new parameter file "data.autodiff" (inAdExact
1334     previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
1335     - add file "data.autodiff" in all verification/*/input_ad/ directories.
1336 jmc 1.1682 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
1337     mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
1338 heimbach 1.1680 o verification/tutorial_tracer_adjsens/
1339     - add extra sub-verification which uses "SOM" advection scheme
1340     (2nd Order-Moment Advection Scheme, Prather Limiter) with
1341 jmc 1.1681 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
1342 heimbach 1.1680 and in data:
1343 jmc 1.1681 multiDimAdvection=.TRUE.,
1344     tempAdvScheme=81,
1345     saltAdvScheme=81,
1346 gforget 1.1683 o model/src:
1347     - introduce ALLOW_BALANCE_RELAX which allow the removal
1348     of the global mean of relaxation terms by setting
1349     balanceThetaClimRelax and balanceSaltClimRelax
1350 jmc 1.1684 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
1351 gforget 1.1683 This case is now treated appropriately in seaice_growth.F
1352     o pkg/seaice:
1353 jmc 1.1684 - do balanceEmPmR and balanceQnet based on the net fluxes
1354     (SItflux) that enter the ocean+ice system rather than QNET
1355     and EMPMR. Works best in real fresh water.
1356     - SIatmFW, SIatmQnet, and SItflux computations had to be moved
1357     out of the diagnotics bloc, and stored in global arrays.
1358 heimbach 1.1680
1359 jmc 1.1679 checkpoint63o (2012/06/29)
1360 jmc 1.1678 o vertical mixing schemes:
1361     - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
1362     - replace computation of density (in Function STATE1, opps_calc.F) by a call
1363     to S/R FIND_RHO_SCALAR
1364     - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
1365     and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
1366     affects output (vermix.ggl90) at truncation level.
1367 jmc 1.1677 o testreport:
1368     - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
1369     (nSx,nSy) for the number of threads (from eedata.mth)
1370 jmc 1.1676 o model/src:
1371     - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
1372     related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
1373 heimbach 1.1675 o verification/tutorial_tracer_adjsens/
1374     - compile with ALLOW_CG2D_NSA
1375     - run with nonlinFreeSurf=3
1376     - update reference output_adm.txt
1377 jmc 1.1674 o tools/genmake2:
1378     - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
1379     refine usePROFILES switching off (only when NetCDF is not available).
1380 jmc 1.1673 o verification (atmospheric set-up):
1381     - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
1382 gforget 1.1672 o pkg/profiles : refine profiles and files handling.
1383     o model/src and pkg/ecco : introduce run-time switch usePROFILES.
1384 gforget 1.1671 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
1385     - changes to use model/src/the_main_loop.F rather than the ecco version
1386     in ecco type adjoint runs.
1387 jmc 1.1670 o model/src:
1388 jmc 1.1673 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
1389     - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
1390     - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
1391     o model/src:
1392     - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
1393 jmc 1.1670 update output of test experiment bottom_ctrl_5x5.
1394 jmc 1.1669 o pkg/generic_advdiff:
1395     - implement vertical bi-harmonic diffusion (for now, only for T & S and
1396     only explicitly).
1397 heimbach 1.1668 o verification/bottom_ctrl_5x5/
1398     update reference output (results changed quite some time ago,
1399     not sure when; but new reference results look ok in terms of grdchk)
1400 heimbach 1.1667 o verification/1D_ocean_ice_column/
1401     For verification purposes, the exact adjoint rather than an approx.
1402     should be used (e.g., to comare against F.D. or TLM).
1403     removed autodiff_inadmode*_ad.F routines in code_ad/
1404     Update results/ accordingly.
1405 jmc 1.1666 o pkg/cal:
1406     - change cal_getdate.F so that output date is function of input time only
1407     (less ambiguous, not mixed up with input iteration number).
1408     - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
1409 jmc 1.1665 o pkg/diagnostics:
1410     - implement calendarDumps also for stats-diags
1411     - implement calendarDumps also for snap-shot output (negative freq)
1412     - for now, ignores calendarDumps if non-zero phase-lag.
1413    
1414 jmc 1.1664 checkpoint63n (2012/06/04)
1415 jmc 1.1662 o model/src:
1416     - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
1417     between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
1418 jmc 1.1663 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
1419     similar to calc_r_star.F); update results of experiment internal_wave and
1420 jmc 1.1662 tutorial_global_oce_in_p (affected @ truncation level).
1421     o pkg/shelfice:
1422     - add parameterisation of advective-diffusive flux into the ice shelf
1423 mlosch 1.1661 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
1424     - simply eps3/3a computation
1425 jmc 1.1660 o eesupp:
1426     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
1427     between tiles, just fill-in edges assuming locally periodic subdomain) and
1428     add corresponding exchange subroutines (EXCH0);
1429     - new CG-solver version (_EX0) for disconnected-tiles special case.
1430 jmc 1.1659 o model/src (CG-solvers):
1431     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
1432     (similar final residual output and max-Iter number as with standard version);
1433     - allows to store and use lowest-residual solution (standard & _SR versions);
1434     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
1435     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
1436     o eesup/src:
1437     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
1438     ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
1439 heimbach 1.1658 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
1440    
1441 jmc 1.1657 checkpoint63m (2012/04/27)
1442 jmc 1.1656 o pkg/shelfice:
1443     - account for partical cells in surface level below ice-shelf for hydrostatic
1444     pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
1445 jmc 1.1654 o ad test experiments:
1446     - update and rename to "ad_optfile.local" local AD-optfile specific to a
1447     particular adjoint verification experiment (in verification/*/code_ad/)
1448 heimbach 1.1653 o pkg/seaice & pkg/exf:
1449 jmc 1.1654 - Part two of ECCO-CLIVAR code merges.
1450 heimbach 1.1653 Completes merge of seaice area relax. code.
1451     Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
1452     to be set in EXF_OPTIONS.h since this pkg controls its I/O
1453     (and avoids second CPP option in SEAICE_OPTIONS.h)
1454 jmc 1.1654 - change default value of costIceStart & costIceEnd to a valid date.
1455 dimitri 1.1655 - add snowPrecip to HSNOW in seaice_growth
1456 jmc 1.1652 o pkg/ptracers:
1457     - move ptracers summary and setup check into separated S/R ; add a check for
1458     valid PTRACERS_Iter0 value (error+stop or just warning).
1459 jmc 1.1651 o pkg/cal (+ pkg/ecco):
1460     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
1461     as input; and for AD, unless both are not differentiable (e.g., k index)).
1462 jmc 1.1650 o model/src:
1463     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
1464     is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
1465     temporary set to usingZCoords value (to be changed to F when using shelfice).
1466     - hydrostatic pressure: implement partial cell near the surface also for
1467     Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
1468     usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
1469     o pkg/ctrl/ctrl_init.F:
1470     - add a formal parameter to s/r ctrl_init_rec to print
1471 mlosch 1.1649 xx_$(ctrl_valiable)_file for easier debugging
1472     - move call of cal_* routines into the if-block where they are really
1473 jmc 1.1650 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
1474 mlosch 1.1649 to specify a startdate
1475 jmc 1.1648 o pkg/seaice:
1476     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
1477     global_ocean.cs32x15/code versions).
1478     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
1479     verification experiment global_ocean.cs32x15.seaice and update results.
1480 jmc 1.1647 o pkg/exf:
1481     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
1482     (according to useExfYearlyFields).
1483 jmc 1.1646 o pkg/cal:
1484     - move calendar setting & summary (previously in cal_readparams.F) into new
1485     S/R CAL_INIT_FIXED to be called later in the initialisation process, once
1486     length of the simulation is set (after SET_PARMS call); This is an attempt
1487     to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
1488     - For safety: keep a record of pkg/cal parameter settings status
1489     to allow to STOP if one pkg/cal S/R is called too early.
1490 jmc 1.1647 - add a stop in all basic pkg/cal subroutines if called before setting is done.
1491     - modify cal_getdate.F: stop when nothing was returned;
1492     if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
1493     this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
1494 jmc 1.1646
1495 jmc 1.1645 checkpoint63l (2012/04/04)
1496 jmc 1.1644 o pkg/bbl:
1497     - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
1498     update global_with_exf output.yearly.txt file.
1499 jmc 1.1643 o pkg/cal:
1500     - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
1501     - remove 2 unsused and very short (1 line only) functions ;
1502     - remove unsused subroutines from AD-Diff list.
1503 jmc 1.1642 o model/src:
1504     - start to implement clean wait to stop in initialization S/R (config_check.F,
1505 jmc 1.1645 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
1506 jmc 1.1642 o folowing PRINT_MESSAGE changes:
1507     - remove reminder multiple print to the same file (STDOUT) when multi-threads.
1508 dimitri 1.1641 o pkg/bbl:
1509     - modification so it can work with z*
1510     - replace deltaT with dTtracerLev(k) for asynchronous time stepping
1511     - global_with_exf/input.yearly verification; changes output.yearly.txt
1512 jmc 1.1639 o eesupp/src:
1513     - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1514     writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1515     - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1516     # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1517     - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1518     - when using MPI, always set usingMPI=T ; set default accordingly and stop
1519     if not consistent.
1520     - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1521     argument is zero (in case called within single-thread section).
1522 jmc 1.1638 o pkg/fizhi:
1523     clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1524     in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1525 jmc 1.1637 o pkg/exch2:
1526     - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1527     activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1528     - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1529     but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1530     with bad ones coming from a not-yet-updated halo.
1531     This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1532 dimitri 1.1636 o pkg/frazil:
1533 jmc 1.1637 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1534     http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1535 mlosch 1.1635 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1536 heimbach 1.1634 o verification/lab_sea
1537     * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1538     * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1539     * nTimeSteps 3 -> 4
1540     * changed reference output accordingly
1541     o pkg/ctrl:
1542     * fix ctrl_get_gen for xx_sst, xx_sss
1543 jmc 1.1632 o pkg/fizhi:
1544     - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1545     update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1546 jmc 1.1633 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1547     fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1548     clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1549 jmc 1.1631 o pkg/gmredi:
1550     - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1551 jmc 1.1630 o pkg/fizhi:
1552     - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1553     (old)aces open64 tuv test.
1554 dimitri 1.1628 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1555 jmc 1.1629 o pkg/mom_vecinv:
1556     - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1557     set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1558     with non-lin free-surf).
1559     o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1560     in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1561 mlosch 1.1627 some compilers (gfortran 4.6.0 on MacOS)
1562 jmc 1.1626 o momentum:
1563     - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1564     & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1565     fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1566    
1567 jmc 1.1625 checkpoint63k (2012/03/17)
1568 jmc 1.1624 o model/src:
1569     - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1570     flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1571     - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1572     (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1573 jmc 1.1622 o model/src: solve_*diagonal.F
1574     - replace division with multiplication by inverse (similar to original version)
1575 jmc 1.1623 update output of AD exp. global_ocean.90x40x15.
1576 jmc 1.1622 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1577     to enable the use of the vectorized & differentiable solve_tridiagonal.F
1578 jmc 1.1623 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1579     vertical advection (to get solve_tridiagonal tested in AD mode).
1580 jmc 1.1622 o pkg/seaice: ECCO-CLIVAR merge:
1581     1. seaice AREA relaxation
1582 heimbach 1.1621 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1583     * runtime flag: SEAICE_tauAreaObsRelax
1584 jmc 1.1622 2. modified global mean cost imbalance code: CPP option
1585     ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1586 heimbach 1.1620 o another iteration on solve_*diagonal.F
1587 jmc 1.1622 Make choices independent of AUTODIFF
1588     Default will be the adjoinable vectorized version.
1589     Alternative choices are:
1590     * non-adjoinable original version with low memory footprint:
1591     #define SOLVE_DIAGONAL_LOWMEMORY
1592     * still adjoinable but does not vectorize (k as inner-most loop):
1593     #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1594 jmc 1.1619 o testreport
1595     - add option to use a home made wrapper around "make"
1596     - remove MITGCM_IEEE env. variable (no longer active)
1597 mlosch 1.1618 o pkg/shelfice
1598     - improve computation of friction velocity for velocity dependent
1599     exchange coefficients: include velocities into SHELFICEBoundaryLayer
1600     block to average velocities vertically
1601     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1602 heimbach 1.1617 o Modify diagonal solvers, now three versions (upon request):
1603     #ifndef SOLVE_DIAGONAL_AUTODIFF
1604     1. default version (dating back a while ago)
1605     #else /* def SOLVE_DIAGONAL_AUTODIFF */
1606     # ifdef SOLVE_DIAGONAL_KINNER
1607     2. adjoinable version with k-innermost loop (G. Forget)
1608     # else
1609     3. adjoinable vectorized version of 2.
1610     # endif
1611     #endif /* SOLVE_DIAGONAL_AUTODIFF */
1612     All flags are currently set within routines, but could/should be moved to CPP-options.
1613     Array bounds for 1. are as before, for 2.,3. cover the entire domain
1614     (could be changed for 1. too).
1615 jmc 1.1616 o verification/lab_sea (fwd):
1616     - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1617     use 7 categories (except hb87), new solve4temp params (except salt_plume),
1618     constant salinity (=4) or variable salinity (salt_plume) done through
1619     SItracer.
1620 jmc 1.1615 o pkg/seaice:
1621     - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1622     - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1623     SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1624     from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1625     SEAICE_freeze got retired) but already better than previously with
1626     SEAICE_freeze=123456.7 deg.C;
1627     - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1628     (safer multi-threaded setting); always set SEAICEuseEVP;
1629     - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1630     SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1631     stop if multiple specifications for the same coeff; make sure default
1632     SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1633 jmc 1.1614 o pkg/obcs:
1634     - allow to switch to upwind 1rst order advection scheme for the advective
1635     flux computation at the open-boundary; disabled for adjoint built.
1636 jmc 1.1613 o pkg/ptracers:
1637     - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1638     - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1639     - add parameter to decide when to start a tracer; use internal flag to
1640     know which tracer to step-forward; switch this internal flag at the top
1641     of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1642     for adjoint built.
1643 jmc 1.1612 o pkg/seaice:
1644     - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1645     - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1646     - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1647 jmc 1.1611 o pkg/ecco:
1648     - fix writing of output file DiagnosCost_ClimSalt/Theta
1649     and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1650 jmc 1.1612 o pkg/seaice:
1651 jmc 1.1610 - add missing initialisation of COR_ICE array in dynsolver.F
1652     - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1653     compiled either way, and is tested in all exps (multidim was only tested
1654     in lab_sea ad before).
1655     - cosmetic change to prepare for future addition of ITD. no change to results.
1656     no defaults change.
1657 gforget 1.1609 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1658 jmc 1.1610 - by lack of adequate verification experiments, I further used custom versions
1659     of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1660     should be correct.
1661 gforget 1.1609 - avoid recomputations in ad.
1662 jmc 1.1608 o array initialisation in adjoint mode:
1663     1) pkg/mom_common/mom_calc_ke.F:
1664     add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1665     The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1666     part this initialisation is gone, resulting in Floating Point Exception
1667     (caught by open64 compiler with debug option).
1668     2) model/src/convective_weights.F
1669     set output convectCount over the full array range (instead of doing
1670     an update): this fix a similar issue when called within recomputation (adjoint)
1671     which could by-pass the initialisation (normally done in the caller S/R).
1672     o pkg/seaice:
1673 gforget 1.1604 - final version of turbulent flux params, as agreed at MIT ice meet:
1674     SEAICE_mcPheePiston (default is ~ 0.000875)
1675     SEAICE_mcPheeTaper (default is 0.)
1676     SEAICE_frazilFrac (defualt is 1.)
1677     SEAICE_mcPheeStepFunc (default is false)
1678 dimitri 1.1605 - changes results at trunction error level
1679     - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
1680 jmc 1.1608 o added pkg/frazil:
1681     - see frazil_description.tex for details
1682 dimitri 1.1607 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
1683 mlosch 1.1602 o pkg/shelfice/shelfice_thermodynamics.F
1684 jmc 1.1608 - fix exponents for velocity dependent exchange coefficients: change
1685 mlosch 1.1602 from 2/3(=0) to 0.66666666666666667
1686 jmc 1.1608 - move computation of velocity dependent exchange coefficients into
1687 mlosch 1.1602 separate loop, so that it applies to both thermodynamics
1688     - move some divisions by constants out of loops
1689    
1690 jmc 1.1601 checkpoint63j (2012/02/16)
1691     o pkg/seaice:
1692     - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
1693     - SItracer: added run time params, and allow coupling to ocn salinity.
1694 jmc 1.1599 o pkg/seaice: remove (almost) all divisions by constants within loops
1695     in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
1696 mlosch 1.1598 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
1697 jmc 1.1599 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
1698     output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
1699     o pkg/seaice :
1700 jmc 1.1601 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
1701     = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
1702 gforget 1.1596 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
1703 jmc 1.1599 - add permanent SItflux diag that corresponds to TFLUX but includes
1704 jmc 1.1601 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
1705 jmc 1.1599 - allow activation/testing of a fix for suspected missing term in
1706 jmc 1.1601 ocn-ice heat budget (to be confirmed). To test this, you want to
1707     undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
1708     SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
1709 gforget 1.1596 - no change in results, fwd or ad.
1710 jmc 1.1601 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
1711 jmc 1.1599 - switch to variable freezing point.
1712 gforget 1.1595 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
1713     - bug fix : the sublimation term that was missing is now activated.
1714     Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
1715 jmc 1.1599 - bug fix : flooding sign term for SIsal0.NE.0.
1716 gforget 1.1595 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
1717     o pkg/seaice:
1718     - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
1719 jmc 1.1601 is now the default, and the old default constant freezing point is recovered
1720     with SEAICE_tempFrz0 = -1.96,
1721     SEAICE_dTempFrz_dS = 0.,
1722     - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
1723 gforget 1.1595 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
1724 jmc 1.1599 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
1725 jmc 1.1601 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
1726 jmc 1.1599 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
1727 jmc 1.1601 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1728 jmc 1.1599 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
1729 jmc 1.1601 seaice_growth r149 for legacy branch (no results change).
1730     - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1731     from I. Fenty).
1732     - results did not change except for global_ocean.cs32x15, mostly due to the
1733     switch to variable freezing point (see above item for detail).
1734 jmc 1.1594 o pkg/thsice:
1735     - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1736     seawater freezing in thsice_calc_thickn (not used).
1737 gforget 1.1593 o pkg/seaice: turbulent flux term specification via run time params.
1738     - replace CPP switches with run time switches to facilitate testing
1739 jmc 1.1601 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1740     GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1741 gforget 1.1593 - added runtime parameter : SEAICEturbFluxFormula
1742     - move Mcphee constants to SEAICE_PARAMS.h
1743     - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1744 jmc 1.1601 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1745     remove seaice_summary call (moved to seaice_init_fixed)
1746 jmc 1.1594 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1747     SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1748 jmc 1.1601 - seaice_summary.F : add missing report of read turbulent flux term set up
1749     and SITRACER.
1750     - seaice_check.F : check range; inform and stop if retired CPPs are used
1751     (incl. SEAICE_AGE).
1752 jmc 1.1594 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1753 jmc 1.1601 CPP switch, same computation as before for the different options.
1754 gforget 1.1593 - change results at the truncation level.
1755 jmc 1.1592 o pkg/seaice:
1756     - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
1757     useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
1758     SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
1759     - update verification/*/input*/data.seaice:
1760     to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
1761     code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
1762     and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
1763     set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
1764 jmc 1.1591 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
1765     - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
1766     algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
1767     difference in results only due to machine truncation.
1768     - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
1769     MaykutPolySatVap; keep MIN_LWDOWN.
1770     - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
1771     - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
1772     + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
1773 jmc 1.1590 o pkg/salt_plume:
1774 jmc 1.1591 - isolate saltPlumeFlux array exch into a specific S/R called from
1775     do_oceanic_phys.F
1776     - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
1777 jmc 1.1590 o verification:
1778 jmc 1.1591 - move untested set-up to MITgcm_contrib/verification_other.
1779 jmc 1.1588 o pkg/seaice:
1780 gforget 1.1589 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
1781     o pkg/seaice:
1782 jmc 1.1588 - seaice_solve4temp.F (keeping results unchanged):
1783     * add 2 future run-time params to select which saturation vapor pressure
1784     formula is used and how post-iteration fluxes are set.
1785     Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
1786     * New piece of code (not used) to update surf. atmos. heat flux F_ia using
1787     the linearized expression to stay consistent with tsurf finding.
1788     - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
1789     can be < 0.
1790 jmc 1.1587 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
1791     - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
1792     conductive heat flux F_c , and add it explicitly when updating tsurf as
1793     solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
1794     so that now F_ia has a consistent meaning through the entire routine.
1795     This causes differences at truncation level: update output of fwd exp.
1796     global_ocean.cs32x15.seaice.
1797 jmc 1.1585 o pkg/seaice:
1798 jmc 1.1586 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
1799     of arrays, sign/direction of fluxes; no effect on results.
1800     - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
1801     in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
1802     note: this should have been done before changing celsius2K default.
1803     - to keep results unchanged, add back old value of celsius2K in verification
1804     exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
1805     - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
1806     SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
1807     value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
1808     freezing temp is consistent with value in seaice_growth.F ; this causes
1809     differences at machine truncation level: update lab_sea AD output (3/4).
1810     o pkg/seaice:
1811 jmc 1.1585 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
1812     and climsst/sss even when using seaice (to prevent calculation that might
1813     use SST on land); does not affect any verification exp.
1814     - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
1815     of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
1816 mlosch 1.1584 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
1817     over land (non-legacy code)
1818 jmc 1.1585 o vectorize salt_plume package:
1819 mlosch 1.1583 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
1820     - this code computes plumebk everywhere (also over land), thus requires
1821     code to avoid divisions by zero and catch the case of kLev=Nr.
1822     - efficiency of salt_plume_frac is still sub-optimal
1823 jmc 1.1582 o tools (genmake2):
1824     - fix makefile NAME specification (option: -makefile NAME) by adding
1825     "-f $MAKEFILE" in few places where it was missing including makedepend
1826     command (contribution from Paul).
1827    
1828 jmc 1.1581 checkpoint63i (2012/01/24)
1829 jmc 1.1579 o model/src:
1830 jmc 1.1581 - add factorized versions of some EOS code to find_rho.F,
1831 mlosch 1.1580 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
1832 jmc 1.1581 o model/src:
1833 jmc 1.1579 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
1834     - change default celsius2K from 273.16 to 273.15
1835     - to keep results unchanged, add back old value of celsius2K in verification
1836 jmc 1.1581 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
1837     global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
1838 mlosch 1.1578 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
1839     to make TAF generate vectorizable code
1840     o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
1841     Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
1842     have flags that do this more efficiently.
1843 mlosch 1.1577 o pkg/diagnostics/diagstats_calc.F
1844     - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
1845 jmc 1.1576 o pkg/obcs (with exch2):
1846     - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
1847     and remove code (in obcs_readparms.F) which was based on EXCH of indices
1848     (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
1849 jmc 1.1574 o pkg/exf and seaice exp:
1850     - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
1851     so that switching off area & heff advection flags does not affect results.
1852     - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
1853 jmc 1.1575 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
1854     EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
1855     results of verification experiments: 1D_ocean_ice_column(fwd),
1856     global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
1857     and offline_exf_seaice (all 4).
1858 jmc 1.1573 o pkg/seaice:
1859     - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
1860     remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
1861     - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
1862     but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
1863     not multi-dim advection;
1864     - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
1865     SHORTWAVE_HEATING #undef.
1866 mlosch 1.1571 o optim: make Makefile more robust (?)
1867 heimbach 1.1572 o pkg/obcs:
1868     * fix treatment of obcs_read_pickup for TAF
1869 jmc 1.1573 o pkg/shelfice:
1870 heimbach 1.1572 * add missing initialisation of num_shifwflx
1871     * new adjoint verification exp. for isomip
1872     * change Prandtl and Schmidt numbers from generic formulations
1873 jmc 1.1573 (in terms of model diffus. and visc.) to separate runtime
1874 heimbach 1.1572 parameters, with Holland and Jenkins (1999) default values.
1875 jmc 1.1570 o pkg/exf (interpolation):
1876     - extended input field (2 rows) near the N & S poles:
1877     * fill in with the symetric value (when even Nb of data in longitude)
1878     * add average value at the poles only for scalar quantities ; for vector
1879     component interpolation, skip the averaging and keep duplicated values,
1880     unless the 2 components have same location (uvInterp=T) in which case
1881     interpolate the 2 components together using S/R EXF_INTERP_UV.
1882     - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
1883     together: this allows to account properly for local orientation when
1884     averaging at N & S pole.
1885     - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
1886     exf-interpolation near N & S poles. Undef by default.
1887     - add debug check/print on 1rst iter if debugLevel >=2.
1888 jmc 1.1569 o pkg/exf:
1889     - change masking flags definition (no longer "parameter"), put them in
1890     common block and set them in S/R EXF_INIT_FIXED.
1891     - change recognized masking flag from s,u,v to c,w,s since the mask
1892     to use (maskC,W,S) depends on position on model grid and has little to
1893     do with scalar/vector difference; fix masking if using P-coordinates.
1894     - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
1895     and update results of exp. global_with_exf (x2).
1896     - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
1897 mlosch 1.1568 o pkg/obcs
1898     - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
1899 jmc 1.1567 o pkg/exf (interpolation):
1900     - assume periodicity in X only if input field cover full longitude range.
1901     - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
1902     and should vectorise).
1903     - fix input lat of the 2 added row (in case we provide N.pole data).
1904    
1905 jmc 1.1565 checkpoint63h (2011/12/30)
1906 jmc 1.1566 o pkg/seaice:
1907     - change declaration of UVM from _RL to _RS in order to get B-grid
1908     uIce,vIce monitor when _RS = real*4
1909 jmc 1.1564 o pkg/offline:
1910     - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
1911     - compute vertical velocity if not read from file (switch on exactConserv
1912     & staggerTimeStep);
1913     - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
1914 jmc 1.1563 o verification:
1915     - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
1916     with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1917     fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1918     - update output of exp. global_ocean.cs32x15.viscA4 after changing
1919     grid-file angles (used here for coriolis-3d);
1920     - remove (or gzip) few files not needed to run fizhi-cs experiments.
1921 jmc 1.1567 o pkg/exf (vector interpolation):
1922 jmc 1.1562 - rotate vector component toward local grid-axis orientation using grid-angles
1923     (stored in GRID.h) instead of locally computed rotation angle; keep old code
1924     available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1925     o pkg/seaice:
1926     - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1927     undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1928 jmc 1.1561 o pkg/PKG_OPTIONS.h files:
1929     - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1930     outside of the #ifdef ALLOW_THISPKG / #endif block.
1931     - update verification/*/code/PKG_OPTIONS.h files.
1932 mlosch 1.1560 o add a verification experiment (offline_exf_seaice/input.seaice) that test
1933     the B-grid LSOR solver
1934 mlosch 1.1559 o pkg/seaice: sort out emissivity and long wave radiation step 2:
1935 jmc 1.1561 - add emissivity for snow and ice as new run-time parameters
1936     (unfortunately) that default to the corresponding exf values; this
1937 mlosch 1.1559 changes results in most verification experiments so that for backward
1938     compatibility these parameter have to be set explicitly to inconsistent
1939 jmc 1.1561 values (ugly);
1940 mlosch 1.1559 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1941     emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1942     until we agree how to handle this bug properly
1943 jmc 1.1557 o pkg/exf (interpolation):
1944     - add a set of run-time param ({inputfield}_interpMethod), one for
1945     each interpolated input field, to select the interpolation method
1946     with a value of zero switching off the interpolation;
1947     - print interpolation parameters to standard output;
1948     - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1949     (to use instead runoff_interpMethod=0 in data.exf).
1950 jmc 1.1558 - simplify default setting of interpolation parameters (for all fields,
1951     set position to match model grid cell-center position, leading to trivial
1952     interpolation in case of regular Lat-Lon grid) and fix for the case of
1953     non-uniform delY.
1954 jmc 1.1557 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1955 mlosch 1.1555 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1956 jmc 1.1557 this factor is absolutely required, because the lw exitance (= out-going
1957     long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1958 mlosch 1.1555 where the reflectivity rho = 1-emissivity for conservation reasons. Once
1959     this is established, we can remove the CPP-Flag (if we want to).
1960 jmc 1.1557 o pkg/seaice:
1961 mlosch 1.1556 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1962     ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1963 mlosch 1.1554 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1964     what the name implies (and not emissivity*BoltzmannConstant), this means
1965 jmc 1.1557 the old default value of 5.5e-8 now means
1966     5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1967 mlosch 1.1554 S/R exf_readparms
1968     - FV-discretization of the B-grid LSOR solver, turn on with
1969 mlosch 1.1555 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1970     of the calling routine dynsolver, so that B and C-grid code look a
1971     little more alike.
1972 mlosch 1.1556 - fix index bugs in ostres.F (B-grid code)
1973 mlosch 1.1553 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1974 mlosch 1.1552 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1975     default for SEAICE_emissivity, if useEXF; requires setting a wrong
1976     parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1977     backward compatiblity
1978     o model/src: use sigmaR in calc_ivdc
1979    
1980 jmc 1.1551 checkpoint63g (2011/12/16)
1981 gforget 1.1550 o pkg/seaice/seaice_growth.F:
1982     fix heat conservation of the coupled ocean-seaice system.
1983     when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1984     solid vs liquid water treatment is resolved via QNET.
1985     o pkg/seaice/seaice_growth.F:
1986     add missing term for sublimation in saltFlux, which was breaking conservation.
1987     o pkg/seaice/seaice_model.F:
1988     Remove this patholigical case treatment in evolution branch,
1989     where it is un-necessary and breaks conservation.
1990 jmc 1.1557 Update global_ocean.cs32x15/results accordingly for
1991     output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1992 jmc 1.1549 o model/src:
1993     useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1994     external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1995     o pkg/obcs:
1996     modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1997     tendency for temperature and salinity that is then applied to update
1998     theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1999     horizontal advection and diffusion contributions on the boundary (in
2000     S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
2001     removing the mask in S/R timestep_tracer. The advantage of this approach is
2002     that the updated tracer values include contributions from the surface
2003     forcing and vertical diffusion.
2004 mlosch 1.1548 This modification changes exp4.stevens because of vertical diffusion.
2005 jmc 1.1545 o model/src:
2006 jmc 1.1547 change non-curvilinear grid setting to also work with exch2 + blank tiles:
2007     - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
2008     face dimensions.
2009     - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
2010     as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
2011     and INI_SPHERICAL_POLAR_GRID.
2012     change test-experiment global_ocean.90x40x15:
2013     - split the domain in many more tiles (9x4 tiles of 10x10 each);
2014     - switch to exch2 and remove 1 blank-tile (but only for MPI test).
2015     - update results of both test (std & dwnslp).
2016 jmc 1.1549 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
2017 mlosch 1.1548 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
2018 jmc 1.1547 o model/src:
2019 jmc 1.1546 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
2020     and fix initialisation when using sigma-coords.
2021     o model/src:
2022     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
2023     to their current value at the beginning of forward_step.F": add a new run-time
2024 jmc 1.1545 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
2025     - set doResetHFactors=T in the following test exp:
2026     global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
2027     global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
2028     and tutorial_global_oce_in_p (nonLinFS in p)
2029 mmazloff 1.1543 o pkg/ecco
2030     - added IES cost term
2031 jmc 1.1542 o verification/advect_xz
2032     - scale down the depth by 1/100 (from 200 km to just 2.km)
2033     - add secondary test using divergent flow, r-star and implicit vertical advection.
2034 jmc 1.1544 - add note (check_conserve_TS.txt) and matlab script to check global
2035     conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
2036 jmc 1.1542 o pkg/rbcs:
2037     - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
2038 mlosch 1.1541 o pkg/obcs (Stevens BCs):
2039 jmc 1.1542 - fix various problems in the phase speed computations of the Stevens
2040 mlosch 1.1541 boundary conditions:
2041     - sign error for western and southern boundaries,
2042 jmc 1.1542 - time tendencies were underestimated by factor of dTracerLev and some just
2043 mlosch 1.1541 zero (for multidim advection schemes) -> now estimate time tendencies
2044     from difference between previous (n) time level and the one before (n-1);
2045 jmc 1.1542 this requires storing a field per tracer per boundary, also in the pickup
2046 mlosch 1.1541 files.
2047     - replace deltaTmom in cflMer/Zon computation with dTracerLev
2048     - set default phase velocity to cflMer/Zon
2049     - update verification experiment exp4.stevens
2050 jmc 1.1540 o pkg/generic_advdiff (implicit_r):
2051     - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
2052     (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
2053     - fix implicit vertical diffusion or advection with NonLin FreeSurf
2054     (was using current recip_hFacC instead of future recip_hFacC): set future
2055     recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
2056     solver S/R ;
2057     - fill diagnostics of vertical advective fluxes (computed from tendency)
2058     when using implicit vert. advection;
2059     - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
2060     global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
2061     tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
2062     and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
2063     o pkg/diagnostics:
2064     - add diags for T & S tendency which goes through Adams-Bashforth.
2065    
2066 jmc 1.1539 checkpoint63f (2011/11/30)
2067 mlosch 1.1537 o pkg/obcs/obcs_calc_stevens.F:
2068 mlosch 1.1538 - join some loops to reduce number of if-statements
2069 mlosch 1.1537 - fix a bug in code for northern and southern boundaries.
2070 mlosch 1.1536 o pkg/seaice/seaice_init_varia.F
2071 jmc 1.1539 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
2072 mlosch 1.1536 caused zero ice-velocities for the B-grid code
2073 mlosch 1.1535 o pkg/seaice/seaice_init_fixed.F
2074 jmc 1.1539 - fix a bug in the initialisation of the second metric terms
2075 mlosch 1.1535 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
2076     - this affects all seaice configurations with useCurviLinearGrid = .true.
2077     and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
2078     = .true. (default)
2079     - the only verification experiment affected is global_ocean.cs32x15:
2080     icedyn, seaice, and seaice_dynmix (AD)
2081     o pkg/thsice/thsice_diagnostics_state.F
2082     - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
2083     not contain garbage that can lead to surprises in diagstats_calc.F
2084 jmc 1.1534 o model/src:
2085     - move bi,bj loops inside INTEGR_CONTINUITY ;
2086     - call INTEGR_CONTINUITY directly from forward_step.F
2087     (previously called from momentum_correction_step.F)
2088     - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
2089     forward_step.F and pkg/ecco/the_main_loop.F
2090 jmc 1.1533 o model/src/do_oceanic_phys.F:
2091     - reset addMass to zero only if useICEFRONT ;
2092     - separated k-loop for rhoInSitu calculation ;
2093     - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
2094     and at constant T,S (= WdRHOdP);
2095     NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
2096     of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
2097     transport of locally-referenced potential density);
2098     to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
2099 mlosch 1.1532 o gluemnc:
2100     - replace ncrcat with ncks when adding variables to *.glob.nc
2101     - change the way variables without record dimensions are handled so that
2102     files that have variables with and without record variables can be glued:
2103     add a record dimension with a new unique name to be able to differentiate
2104     between variable with and without a-prior record dimensions. Remove
2105     this record dimension before adding the variable to the *.glob.nc file.
2106     This procedure automatically works also for grid.*.nc files that do not
2107     have any record dimension.
2108 jmc 1.1531 o verification/cpl_aim+ocn:
2109     - generate new reference output on baudelaire (gfortran, mpich2) (previously
2110     from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
2111     o pkg/obcs/obcs_calc_stevens.F:
2112 mlosch 1.1530 - add code for northern and southern boundaries.
2113     - reorder some loops to save some operations and so that drFBar can be scalar
2114 jmc 1.1529 o model/src:
2115     - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
2116     truncation) and add diagnostics for Adams-Bashforth tendency increment.
2117     - update test-exp. AD output:
2118     1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
2119     and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
2120     front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
2121     global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
2122     matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
2123     tutorial_global_oce_in_p, tutorial_global_oce_latlon and
2124     tutorial_plume_on_slope.
2125 mlosch 1.1528 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
2126     that vectorises. This code uses 3 extra 2D fields, F90 array assignments
2127     and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
2128     does not even come with an F77 compiler anymore, this should not be
2129     a limitation
2130    
2131 jmc 1.1527 checkpoint63e (2011/11/06)
2132 heimbach 1.1525 o pkg/seaice adjoint of LSR:
2133     - substantially rework STORE dirs.
2134     - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
2135     this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
2136     and only perform SOLV_MAX_FIXED adjoint iters.
2137 heimbach 1.1526 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
2138     always goes to same record, meaning that the last forward field will be
2139     the one used in the adjoint - an approximation.
2140 heimbach 1.1525 - now produces non-zero LSR-related gradients, and acceptable gradients for
2141     An's zonal (x-z) test case (to be checked in)
2142     - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
2143     (but these are screwed up by the thermodynamics in the first place);
2144     reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
2145     output_adm.txt also reflects changes to seaice_lsr
2146 jmc 1.1527 - global_ocean.cs32x15:
2147 heimbach 1.1525 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
2148     (output_adm.seaice.txt was updated)
2149     * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
2150     (output_adm.seaice_dynmix.txt)
2151 jmc 1.1524 o test-exp. exp4+stevens:
2152     - switch off pTracers and nonHydrostatic (restart problems with NH); update output
2153 jmc 1.1523 o pkg/seaice (lsr solver):
2154     - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
2155     update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
2156     - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
2157     - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
2158     into initial guess for linearised solver; use weight ~ (1/err)^2,4.
2159     - compute (with new S/R) and print initial (+ free-driff sol. if available)
2160     and final residual of linearised system.
2161 mlosch 1.1522 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
2162     (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
2163 mlosch 1.1521 o pkg/obcs: Stevens BCs (still only for east and west)
2164     - fix Stevens BCs by using intermediate velocities of previous
2165     time step as "baroclinic" contribution rather velocity of one grid cell
2166     inside the boundaries; more consistent but makes the entire treatment
2167 jmc 1.1523 more complicated, requires new pickup files and two new S/Rs:
2168 mlosch 1.1521 obcs_copy_uv_n and obcs_save_uv_n
2169 jmc 1.1523 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
2170 mlosch 1.1521 (undefined by default)
2171 jmc 1.1523 - silently move computation of some grid factors into separate loops to
2172 mlosch 1.1521 save some recomputations
2173     - add a hack for non-linear free surface
2174     - add a verification experiment to exp4 that tests this code
2175 mlosch 1.1520 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
2176    
2177 jmc 1.1519 checkpoint63d (2011/10/25)
2178 jmc 1.1516 o pkg/obcs + seaice-dynamics:
2179     - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
2180     solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
2181     values (consistent with an implicit method).
2182     - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
2183     return to older implementation (same results as before); note that none of
2184     the "experimental" OBCS_SEAICE options are implemented in the new version.
2185 jmc 1.1517 - switch test exp. seaice_obcs to use new version (update output).
2186 jmc 1.1516 o pkg/seaice:
2187     - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
2188     - add parenthesis in Water-Ice drag calculations (evp & lsr);
2189     - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
2190 jmc 1.1515 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
2191     - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
2192     and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
2193 dfer 1.1514 o pkg/layers:
2194     - Include potential density as new coordinate (Thanks to David Munday)
2195     o pkg/dic:
2196     - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
2197     carbonate computation/output to CALC_PCO2_APPROX
2198 mlosch 1.1518 o pkg/generic_advdiff
2199 jmc 1.1519 - make TAF generate code that vectorizes:
2200 mlosch 1.1518 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
2201 jmc 1.1519 o model/src:
2202     - improve vectorization also for adjoint code of
2203 mlosch 1.1513 solve_tridiagonal and solve_pentadiagonal. As this requires up to
2204     5 new 3D-fields, this code is only turned on for the combination of
2205 mlosch 1.1518 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
2206     for singular matrix check (only for TARGET_NEC_SX).
2207 mlosch 1.1513 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
2208 jmc 1.1516 ALLOW_AUTODIFF. This flag now needs to be set outside of
2209 mlosch 1.1513 solve_tri/pentadiagonal.F
2210 jmc 1.1512 o pkg/exf:
2211     - fix previous modif in exf_readparms.F (revision 1.66: treatment of
2212     optional namelist EXF_NML_OBCS).
2213     - add many debug-print (to trace down where pkg/cal error msg comes from)
2214 mlosch 1.1511 o pkg/mom_vecinv/mom_vi_hdissip.F
2215     - rearrange loops so that vectorization is improved and in particular
2216 jmc 1.1512 the adjoint routine vectorizes. The code is a little longer now, but I
2217     think easier to read.
2218 mlosch 1.1511 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
2219 jmc 1.1510 o pkg/seaice:
2220     - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
2221 jmc 1.1509 o pkg/exch2:
2222     - alternative code (without tile x tile matrix) for cumulated (global) sum;
2223     used as default; keep using matrix version in adjustment.cs-32x32x1.
2224 jmc 1.1508 o tools/build_options:
2225     - after merging some MPI and/or multi-threads specific optfiles so that
2226     the modified default optfile support both built (using genmake2 -mpi
2227     for the MPI built, using genmake2 -omp for OpenMP built),
2228     move now obsolete optfiles to tools/build_options/unsupported/
2229     (add copy of email sent to support list in doc/optfiles_changes.txt)
2230    
2231 jmc 1.1507 checkpoint63c (2011/09/28)
2232 jmc 1.1506 o pkg/ebm:
2233 jmc 1.1507 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
2234 jmc 1.1506 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
2235 heimbach 1.1504 o pkg/seaice (SItracer pickup)
2236     * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
2237     To be done:
2238     - thorough testing of missing fields in S/R seaice_read_pickup
2239     - thorough matching between generic tracers and specific fields used
2240     (e.g. volume-weighted age, area-weighted age, salinity, ...)
2241 jmc 1.1505 o pkg/grdchk:
2242     - all procs calculate and print finite-difference gradient (for testreport)
2243     - change description output used by testreport;
2244     - AD testing: also compare and report Finite-difference gradient;
2245     => update all output_adm*.txt
2246     o test exp. global_ocean_ebm:
2247     - switch back useRealFreshWaterFlux (no problem anymore with run-off);
2248     and turn on exactConserve; update (fwd) output.
2249 jmc 1.1503 o pkg/seaice (LSR):
2250     - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
2251     - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
2252     * identical results with non-CS topology (but save up to half of EXCH calls)
2253     * no much changes in cs-32 verification tests since no ice at face edges
2254     (differences due to convergence criteria, since nb of iterations changed)
2255     * expect some differences on lat-lon-cap grid.
2256     update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
2257 jmc 1.1502 o pkg/exch2:
2258     - add new CPP option to disable Cumul-Sum matrix (to save storage when using
2259     many tiles); until alternative coding is added, just add a stop.
2260 jmc 1.1501 o pkg/kpp:
2261     - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
2262     to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
2263     o optfiles:
2264     - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
2265     into corresponding standard one, which now support different build:
2266     (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
2267     - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
2268 jmc 1.1500 o pkg/obcs (seaice):
2269     - add missing EXCH for uIce,vIce after applying OBCS;
2270     - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
2271     argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
2272     EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
2273     - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
2274     - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
2275     and eedata.mth for MPI and mutlti-threaded testing.
2276 jmc 1.1499 o pkg/flt:
2277     - make FLT EXCH working with multi-threads (and MPI + multi-threads);
2278     - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
2279     - fix pickup and trajectories + profiles output with multi-threads;
2280     - add parameter to select group of fields to write along trajectory and
2281     profile (default unchanged);
2282     - only call PORT_RAND* function when flt_noise <> 0;
2283     - add multi-threaded test for verification exp. flt_example.
2284     o eesupp/src:
2285     - fix S/R ALL_PROC_DIE for MPI+multi-threads.
2286     - USE_OMP_THREADING: check that number of threads (from eedata) matches
2287     actual number (from env.var. setting).
2288 jmc 1.1498 o pkg/ebm:
2289     - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
2290     - add multi-threaded test for verification exp. global_ocean_ebm
2291    
2292 jmc 1.1497 checkpoint63b (2011/08/29)
2293 jmc 1.1496 o pkg/ebm:
2294     - fix sign of runoff;
2295     - update directly forcing fields (Qnet,EmPmR) to use standard
2296     external_forcing_surf.F (remove ebm_forcing_surf.F);
2297     - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
2298     - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
2299     and apply relaxation towards corresponding SST field (2-D map or ZonAver).
2300     - update global_ocean_ebm parameters file data and update output (fwd+ad).
2301 jmc 1.1494 o verification/matrix_example:
2302 jmc 1.1495 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
2303     MPI and mutlti-threaded testing.
2304     o pkg/matrix:
2305     - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
2306     - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
2307     - fix for multi-threaded (remove DATA statement);
2308     - use standard DIFFERENT_MULTIPLE function;
2309     - add MATRIX_OPTIONS.h
2310     o verification/matrix_example:
2311 jmc 1.1494 To allow to split the domain in several tiles, change the domain size
2312     from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
2313     Western side) of land points.
2314     o (*_)write_pickup:
2315     - fix few bugs in mypackage_read/write_pickup.F
2316     - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
2317     array of length 1 (was caught by compiler syntax-check).
2318 jmc 1.1493 o pkg/diagnostics (velocity potential solver):
2319     - fix initialisation of main diagonal matrix (for overlap values)
2320 jmc 1.1492 o tools/build_options:
2321     - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
2322     into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
2323     - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
2324     * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
2325     * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
2326     and use "-devel" testreport option for standard testing on baudelaire.
2327 jmc 1.1491 o pkg/grdchk:
2328     - Assume that all gradient-check position are within the same tile
2329     corresponding to global indices (iGloTile,jGloTile) and that
2330     positions (i,j indices or nbeg) are local to this tile;
2331     - set tile local-indices and proc. number according to tile global-indices;
2332     - remove grdchkwhichproc from namelist (retired param);
2333     - send adjoint gradient to all procs so that all procs print it to STDOUT;
2334     - switch on MPI test for global_ocean.90x40x15 AD test experiment.
2335 dimitri 1.1489 o adding package bbl (Bottom Boundary Layer)
2336     description in MITgcm/pkg/bbl/bbl_description.tex
2337     example/test experiment in MITgcm_contrib/bbl
2338 heimbach 1.1488 o adjoint verifications
2339 jmc 1.1490 - changed 5 experiments to multi-tiles
2340 heimbach 1.1488 * global_ocean.90x40x15
2341     * obcs_ctrl
2342     * offline_exf_seaice
2343     * tutorial_dic_adjoffline
2344     * tutorial_tracer_adjsens
2345     changed reference output for those that crossed tile boundaries
2346     (changed choices of gradient check positions)
2347 jmc 1.1490 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
2348 heimbach 1.1488 - temporary bug fix in grdchk_loc.F for obcs
2349 jmc 1.1487 o genmake2 & testreport
2350     - add target "obj" (just for OBJFILES files) to Makefile;
2351     - add option to specify FEXTRAFLAGS on command line.
2352 jmc 1.1486 o pkg/mypackage:
2353     - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
2354    
2355 jmc 1.1485 checkpoint63a (2011/08/02)
2356 jmc 1.1484 o pkg/diagnostics (velocity potential):
2357     - fix velocity-potential calculation when using OBCS: balance net inflow
2358     at each level (new S/R OBCS_DIAG_BALANCE).
2359     - fix some of the problems with OBCS in stream-function calculation.
2360 mlosch 1.1483 o pkg/exf/exf_readparms.F
2361 jmc 1.1484 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
2362 mlosch 1.1483 EXF_NML_OBCS) more consistent, so that you need not have these lists
2363     in data.exf when they are not used.
2364 mlosch 1.1481 o optim/optim_readdata.F:
2365     - add some output about obcs variables that might help debugging
2366 mlosch 1.1482 - add a check about nvarlength
2367 mlosch 1.1480 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
2368 jmc 1.1479 o pkg/diagnostics (velocity potential):
2369     - fix mask for OBCS (still problems in stream-function with OBCS);
2370     - add specific parameter (default = main code CG2D params) for solver;
2371     - in case of poor convergence, use solution corresponding to lowest residual.
2372 mlosch 1.1478 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
2373     adjoint code. In general statements like tmpscal=fld(i,j) are problematic
2374     and should be avoided where possible.
2375 jmc 1.1477 o model/src (rStar):
2376     - include r* effect on reference-state (PhiRef) in totPhiHyd
2377     (so that it's really the potential anomaly at the cell center);
2378     affect solution only if z* with full pressure in EOS.
2379     - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
2380     update output (because of z* in totPhiHyd and viscA4 changes);
2381     - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
2382     @ constant r) until interpolation at constant r is implemented.
2383     o pkg/diagnostics
2384     - fix RCENTER diagnostics in case cell center is not at interface middle
2385 mlosch 1.1476 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
2386     this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
2387     that THETA and SALT are "conservative temperature" and "absolute
2388     salinity"
2389     o pkg/ctrl
2390     - fix computation of endrec in s/r ctrl_init_rec
2391     - ctrl_pack/unpack_*: remove unused variables and some obsolete code
2392 mlosch 1.1475 o pkg/seaice/seaice_growth.F
2393     - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
2394     remove then obsolete STORE directives
2395     - fix STORE directives for tice and tices, so that only the
2396     appropriate part of the fields are stored (and not the entire
2397 jmc 1.1477 field); update global_ocean.cs32x15.seaice AD output.
2398 mlosch 1.1475 - cosmetic changes: adjust CPP flags and indentation for better
2399     legibilty
2400     o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
2401     Chris Wilson)
2402 jmc 1.1474 o pkg/gmredi:
2403     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
2404     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
2405    
2406 jmc 1.1485 checkpoint63 (2011/07/11)
2407 jmc 1.1472 o pkg/exch2:
2408     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
2409     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
2410     (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
2411     increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
2412 jmc 1.1470 o pkg/diagnostics:
2413     - deal with pairs of post-processed diags which are computed together; in
2414     particular, re-order list of diags within 1 file to save 2nd computation.
2415     - add S/R to compute velocity stream-function (called after velocity-potential
2416     calculation) from divergence free transport -> new diagnostics "PsiVEL".
2417 jmc 1.1471 - add parameter to select grid-point location where PsiVEL == 0.
2418 jmc 1.1470 o eesupp/src:
2419     new S/R to calculate cumulated sum on tiled array, corner grid-cell location
2420     (specific S/R needed with exch2 topology - for now, just print an error msg)
2421 heimbach 1.1468 o pkg/shelfice
2422     - Implement friction velocity-dependent transfer coefficients following
2423     Holland and Jenkins, JPO, 1999
2424     Original code by M. Losch with small modifs.
2425     Enable with CPP option SHI_ALLOW_GAMMAFRICT
2426     and runtime flag SHELFICEuseGammaFrict
2427 jmc 1.1467 o verification lab_sea & global_ocean.cs32x15:
2428     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
2429     does not miss some dependencies (but is slower) and also works with many files
2430     (default makedepend limitation for AD built).
2431     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
2432 jmc 1.1466 o pkg/diagnostics:
2433     - add run-time parameter "useMissingValue" (def=False) to fill land-point
2434     (i.e., where mask=0) with MissingValue ; used only in MNC output file.
2435     This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
2436     - Extend the use of "missing_value" setting from data.diagnostics for the case
2437     of counter-diagnostics (where fraction-weight is zero). This applies both to
2438     MNC and MDS output files.
2439 gforget 1.1465 o pkg/seaice/seaice_growth.F:
2440 ifenty 1.1469 - add 'a priori' cap of latent heat flux based on actual mass considerations
2441     when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
2442     non-legacy seaice_solve4temp.
2443     - add diagnostic of the residual sublimation freshwater flux (the freshwater
2444 jmc 1.1470 flux taken from the ocean if the total actual latent heat fluxes exceed
2445 ifenty 1.1469 the maximum)
2446 gforget 1.1465 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
2447     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
2448     - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
2449     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
2450     - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
2451     - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
2452 ifenty 1.1464 o verification 1D_ocean_ice_column:
2453     made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
2454     update results
2455 jmc 1.1461 o pkg/diagnostics:
2456     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
2457     which are not filled-up but computed from other diags ; In this case, the mate
2458     diag points to the primary (filled-up) diag to used for post processing.
2459     - Update Velocity-potential computation using post-processed diag framework.
2460 jmc 1.1463 ==> Change the ordering of fields and time-periods in MDS output file
2461 jmc 1.1462 when using periodic averaging: now writes one time record with the full set
2462     of fields for this time period, then the next time reccord (it used to be
2463     one field with the full set of time records then the next field).
2464 jmc 1.1463 Note: this is now similar to NetCDF (MNC) output file. <==
2465 jmc 1.1461
2466 jmc 1.1460 checkpoint62z (2011/06/21)
2467 heimbach 1.1456 o adjoint monitor:
2468     - Add adjoint monitor output for packages exf, seaice
2469 heimbach 1.1457 and update relevant testreport output
2470 gforget 1.1455 o pkg/seaice:
2471     - re-order diags inits so that they appear in order in available_diagnostics.log
2472     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
2473     area/heff/hsnow preceeding thermodynamic growth/melt.
2474     - modified diag: SIdA; output actual effect, as the description states.
2475     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
2476     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
2477 jmc 1.1459 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
2478 gforget 1.1455 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
2479     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
2480 jmc 1.1459 - added diagnostics for seaice generic tracers (SItr*).
2481 gforget 1.1455 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
2482     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
2483 heimbach 1.1458 I. Fenty: 18-Jun-2011:
2484     Minor changes to seaice package:
2485     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
2486     added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
2487 jmc 1.1459 - Differentiated "regularization variables" from "floor variables"
2488 heimbach 1.1458 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
2489     * hiceMin became SEAICE_hice_reg (old hiceMin)
2490     (with _reg meaning regularization variable)
2491     - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
2492     so as to ensure energy conservation when going between phases
2493 jmc 1.1459 - A22 was not used anywhere
2494 heimbach 1.1458 2) Changed regularization procedure for heffActual and hsnowActual to ensure
2495     well-boundedness and smooth adjoint in seaice_growth.F
2496     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
2497     because the old regularization always set heffActual >= 0.05 cm
2498     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
2499 jmc 1.1459 on AREA when HEFF > 0.
2500     - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
2501     requiring that DISABLE_AREA_FLOOR *not* be defined
2502 heimbach 1.1458 Affected verifications:
2503     - 1D_ocean_ice_column (output.txt output_adm.txt)
2504     - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
2505 jmc 1.1453 o pkg/diagnostics:
2506     - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
2507     - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
2508     (was _RL, now integer) with option = 0 to retrieve all levels.
2509 jmc 1.1454 - add pieces of code to compute velocity potential at each level (new diagnostics
2510     PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
2511     for now, using same params as CG2D (target-resisual, max Nb of iter ...).
2512 jmc 1.1459 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
2513     diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
2514     and in diagnostics_fract_fill.F (do not need a valid pointer for the
2515     diagnostics counter-mate); check that definition of counter-diagnostic
2516     includes a valid counter-mate (in diagnostics_set_levels.F).
2517 jmc 1.1452 o model/src (rStar):
2518     - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
2519     affect solution only if z* with full pressure in EOS;
2520     update output of test-exp global_ocean.90x40x15.
2521     o pkg/seaice:
2522 gforget 1.1451 - introduce siEps=1e-5 parameter
2523     - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
2524     - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
2525 jmc 1.1452 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
2526 gforget 1.1451 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
2527     as well as ice cover age and ridging index (attached to AREA).
2528 jmc 1.1452 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
2529     SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
2530 gforget 1.1451 Up to SItrMaxNum=3 tracers can be used simultaneously.
2531     o pkg/salt_plume:
2532 jmc 1.1452 -introduce SPsalFRAC run time parameter that sets the fraction of the
2533     salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
2534     that gets vertically redistributed (fluxed down) by pkg/salt_plume.
2535 jmc 1.1450 o model debug options:
2536     - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
2537     in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
2538     - Refine debug-msg printing selection (3 new levels):
2539     debugMode : controls printing of debug messages (sequence of S/R calls).
2540     debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
2541     debLevZero = 0 ; /* level of disabled aux. msg printing */
2542     debLevA = 1 ; /* level of minimum aux. msg printing */
2543     debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
2544     debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
2545     debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
2546     debLevE = 5 ; /* level of extensive debug printing */
2547     New debugLevel default: with default debugMode value (=F),
2548     = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
2549     and if debugMode=T, default debugLevel = 4 (debLevD).
2550     Relation with previous settings:
2551     debLevB (=2) corresponds to former debLevA (=1)
2552     debLevD (=4) corresponds to former debLevB (=2)
2553     Note:
2554     a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
2555     b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
2556     to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
2557     - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
2558     detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
2559 jmc 1.1449 o pkg/obcs:
2560     - change OBCSfixTopo default from True to False (should not change the results);
2561     keep OBCSfixTopo=T in verification-exp. seaice_obcs.
2562 jmc 1.1448 o pkg/thsice:
2563     - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
2564     2nd layer seaice sublimation (unlikely to happen)
2565     - use Interior mask for OBCS in thsice_advection.F (similar to what is
2566     done in gad_advection & seaice_advection).
2567 heimbach 1.1447 o adjoint:
2568     bug fix spotted by Gael Forget:
2569     seaice_advection and thsice_advection still had
2570     legacy CPP options to avoid CS corner updates for adjoint
2571 jmc 1.1446 o pkg/seaice:
2572     => Change some of the defaults (2011/05/29):
2573     - change SEAICEuseFluxForm default (from False to True)
2574     - change DIFF1 default (from 0.004 m/s to 0. m/s)
2575     And print warnings if DIFF1 is not set in data.seaice and centered
2576     avection scheme is used without any diffusion.
2577     also:
2578     - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
2579     - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
2580     - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
2581     other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
2582     #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
2583     update results of test exp.:
2584     lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
2585     output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
2586     output_adm.noseaicedyn (SEAICEuseFluxForm=T)
2587     offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
2588     seaice_obcs: output (SEAICEuseFluxForm=T)
2589     and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
2590     for standard fwd & AD lab_sea tests (to keep the same output).
2591 gforget 1.1445 o pkg/seaice/seaice_growth.F:
2592 jmc 1.1446 - use Ian Fenty's capping formulas for actual ice
2593 gforget 1.1445 thickness thoughout EVOLUTION branch.
2594     - put treatment pathological case #2) in CPP brackets
2595     (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
2596 jmc 1.1446 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
2597 gforget 1.1445 o pkg/seaice:
2598     - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
2599 jmc 1.1446 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
2600     also pass fac as a param, which can be 1. (to update the tendency
2601 gforget 1.1445 field) or the time step (to update the field itself).
2602 jmc 1.1446 - seaice_advdiff.F: for multidim, call seaice_diffusion with
2603 gforget 1.1445 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
2604     seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
2605 jmc 1.1446 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
2606 gforget 1.1445 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
2607 jmc 1.1444 o pkg/seaice:
2608     diffusion with centered advection scheme (diffus.F & advect.F):
2609     - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
2610     to just compute the laplacian of input-field.
2611     - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
2612     - fix flux-form version in diffus.F to conserve tracer.
2613     update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
2614     machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
2615    
2616 jmc 1.1443 checkpoint62y (2011/05/26)
2617 gforget 1.1442 o pkg/seaice:
2618 jmc 1.1443 - seaice_growth.F : in EVOLUTION branch, always include
2619 gforget 1.1442 a_QSWbyATM_cover in qnet (as it should be).
2620     - verification/global_ocean.cs32x15 : update results accordingly
2621 jmc 1.1443 (output.seaice.txt output_adm.seaice.txt).
2622 jmc 1.1441 o pkg/seaice + obcs:
2623     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
2624     equivalent of assuming no tracer gradient outside the OB region.
2625     update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
2626     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
2627     after changes above);
2628     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
2629     only at OB location (instead of over a band of OLx width).
2630     o pkg/seaice:
2631     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
2632     (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
2633 jmc 1.1438 o pkg/obcs:
2634 jmc 1.1439 - split header file "OBCS.h" into 4 separated files:
2635     OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
2636     Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
2637 jmc 1.1440 (contain no conditional statement which depends on OBCS options).
2638     - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
2639     to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
2640 jmc 1.1439 o ctrl, cost, grdchk & autodiff pkgs:
2641     - make options file more standard (like other {PKG}_OPTIONS.h file but
2642     with AD_CONFIG.h); clean-up some of the included header files.
2643     o pkg/obcs:
2644 jmc 1.1438 - do not mask tracer when applying OB (tracer == 0 could generate problems)
2645     - apply tracer OB values to tracer field only at OB location (instead of
2646     over a band of OLx width)
2647     - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
2648     - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
2649     obcs_apply_tloc.F & obcs_apply_sloc.F
2650     o obcs in model/src:
2651     - call OBCS_APPLY_W only if NonHydrostatic.
2652     - call OBCS_APPLY_ETA only if NonLinFreeSurf.
2653     - reset dEtaHdt and wVel to zero outside OB interior region ;
2654     - leave tracer unchanged outside OB interior region: This has no effect
2655     on the solution but just to prevent unrealistic tracer value outside OB.
2656     - zero out velocity outside OB interior region: This has no effect on
2657     the solution but just to prevent unrealistic velocity outside OB.
2658 jmc 1.1437 o obcs and non-lin free-surf:
2659     move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
2660     and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
2661     + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
2662     this fixes missing EXCH + get consistent eta OB value (+ fix restart).
2663     update results of test-exp. exp4(nlfs).
2664 jmc 1.1436 o exp4 (nlfs) test-exp:
2665     use OBC for Eta at Western & Eastern OB (to test prescribing Eta
2666     with NonLin-FreeSurf); update output.nlfs.txt
2667 jmc 1.1435 o obcs and 2d/3d solver norm:
2668 jmc 1.1436 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
2669     and outside OB interior region (will allow to place OB further inside the
2670     domain). Depending on the domain, can affects cg2d-Norm (previous
2671 jmc 1.1438 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
2672 jmc 1.1435 and cg3d-Norm (previous Norm was computed before canceling OB terms),
2673     e.g. in tutorial_plume_on_slope.
2674     - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
2675 jmc 1.1433 o pkg rbcs:
2676     - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
2677     - add capability to apply relaxation to horizontal velocity uVel & vVel.
2678 mlosch 1.1432 o pkg/grdchk: add gradient check for control variable xx_shifwflx
2679     o pkg/shelfice/shelfice_init_fixed.F
2680     fix CPP-flag combinations
2681 heimbach 1.1434 o pkg/seaice: Merge iceage code of Pierre Rampal
2682     * update/change/correct ice age calculations
2683 jmc 1.1436 * add age updates for pathological cases
2684 heimbach 1.1434 Probably needs more testing...
2685 mlosch 1.1432
2686 jmc 1.1431 checkpoint62x (2011/05/13)
2687     o pkg/mom_vecinv:
2688 jmc 1.1433 high-order vorticity scheme: use interior masks (maskInW & S)
2689 jmc 1.1431 to zero-out (outside OB) gradient of vorticity.
2690 jmc 1.1430 o verification exp.:
2691     turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
2692     hs94.128x64x5 and seaice_obcs ; update results.
2693 jahn 1.1429 o pkg/obcs:
2694     fix bug in OBeta for YZ sections in obcs_exf_load.F
2695 jmc 1.1430 o pkg/ctrl, pkg/shelfice, and optim:
2696     - add new control variable xx_shifwflx (fresh water flux underneath ice
2697     shelves). This is almost as tedious as obcs-ctrl, because the
2698 mlosch 1.1427 variables needs its own mask.
2699 jmc 1.1430 - add a cost function term that penalizes the deviation of xx_shifwflx
2700 mlosch 1.1427 from the first guess (zero) in analogy to other control variables
2701 heimbach 1.1426 o pkg/shelfice:
2702     - start basic adjoint
2703 jmc 1.1430 o pkg/ctrl:
2704 mlosch 1.1425 - remove extra 2D field "for good measure" when initializing in
2705     ctrl_set_globfld_[xy/xz/yz].F
2706 mlosch 1.1424 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
2707     - improve error messages in ctrl_set_unpack_*
2708 jmc 1.1423 o OBC implementation in momentum:
2709     use interior masks (maskInC,W & S) in momentum S/R:
2710     - multiply divergence, tension and some del^i.u or del^j.v by maskInC
2711     - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
2712     - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
2713     - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
2714     Motivation: fix/clean implementation of OBC with biharmonic-viscosity
2715     (and also with Leith/Smagorinsky harmonic-viscosity).
2716     Update output of experiment dome and exp4 (+nlfs).
2717 jmc 1.1421 o exp4 test-exp:
2718 jmc 1.1422 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
2719     and prescribe time-varying OB (without pkg/exf) for zonal-velocity
2720     at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
2721     time-varying OB at Western-side for wVel (NonHyd); update output.
2722 jmc 1.1421 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
2723 jmc 1.1422 and biharmonic-viscosity ; also use prescribed time varying OB.
2724 jmc 1.1421 o pkg/obcs:
2725     fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
2726 jmc 1.1420 o model/src:
2727     - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
2728     - initialise startTime & nIter0 with unlikely values: allows to set one
2729     from the other without ambiguity.
2730 jmc 1.1419 o seaice_obcs test-exp.:
2731     add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
2732 jmc 1.1418 o pkg/obcs:
2733     - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
2734     no longer needed with maskInC,W,S in pkg/generic_advdiff.
2735 ifenty 1.1417 o pkg/seaice:
2736 jmc 1.1418 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
2737 ifenty 1.1417 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
2738 jmc 1.1418 - fixed bug in the initialization of sea ice salinity variable HSALT
2739 ifenty 1.1417 in seaice_init_varia.F (removed dependence on ICE2WATR)
2740 jmc 1.1416 o fizhi-cs test exp.:
2741     switch reference output convention for these 2 non-standard test-exp,
2742 jmc 1.1418 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
2743 jmc 1.1416 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
2744     reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
2745 jmc 1.1415 o model/inc:
2746     - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
2747     of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
2748 ifenty 1.1414 o pkg/seaice:
2749     - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
2750     o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
2751 ifenty 1.1417 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
2752     and initial HSALT
2753 ifenty 1.1414
2754 jmc 1.1413 checkpoint62w (2011/04/26)
2755 jmc 1.1412 o pkg/mom_fluxform:
2756     - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
2757     - use parameter "sideDragFactor" in no-slip BC side-drag part.
2758     - update output of exp. global_ocean.90x40x15
2759 jmc 1.1411 o pkg/mom_vecinv:
2760     mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
2761 jmc 1.1413 o update seaice exp.:
2762     use more consistent parameter values (remove "backward compatability only":
2763     ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
2764     related to thermodynamics seaice. Update output (fwd+AD) of exp.:
2765     1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
2766 jmc 1.1411 o update test-exp global_ocean.90x40x15:
2767     o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
2768     o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
2769     o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
2770     o turn on zStar & viscA4 in standard set-up (dir input/)
2771     and update output files: output.txt & output.dwnslp.txt
2772 jmc 1.1409 o new AD-test experiment: obcs_ctrl
2773     (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
2774     o pkg/dic:
2775     fix two bugs in handling water vapour pressure in carbonate chemistry
2776     and air-sea fluxes. Found by Val Bennington and Galen McKinley
2777     (add DIC Option = WATERVAP_BUG to recover old results)
2778     update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
2779 dimitri 1.1408 o adding allowInteriorFreezing option to check for water below freezing point
2780     at depth and bring the negative heat anomaly to the surface level
2781 jmc 1.1409 o pkgs _fields_load:
2782     - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
2783     - use new S/R GET_PERIODIC_INTERVAL in pkgs:
2784 jmc 1.1410 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
2785     rbcs to get interpolation weights and time reccord number.
2786 jmc 1.1409 - fix multi-threading in aim_fields_load.F
2787     - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
2788 jmc 1.1407 o external_fields_load:
2789     new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
2790     interpolation weights) to use in a periodic time-series ; do not divide by
2791     time-step to convert to integer:
2792     - this fixes case where externForcingPeriod is not multiple of time-step
2793     (Thanks to Christopher L. Wolfe)
2794     - this fixes case where externForcingPeriod is an odd multiple of time-step
2795     (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
2796     store index of time-record which is currently loaded:
2797     - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
2798     - needed for the adjoint but not yet used because of extensive recomputations;
2799     (to be fixed soon)
2800    
2801 jmc 1.1405 checkpoint62v (2011/04/02)
2802 ifenty 1.1406 o verification/1D_ocean_ice_column added to test Ian Fenty's
2803     pkg/seaice_growth.F modifications for improving sea ice code differentiability
2804 jmc 1.1405 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
2805     (new velocity statistics after changing maskInW & maskInS definition)
2806 jmc 1.1404 o pkg/generic_advdiff with OBCS:
2807     use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
2808     equivalent to assumption of no tracer gradient outside the OB region.
2809     This will affect the results if using obcs+biharmonic diffusion.
2810     update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
2811 jmc 1.1403 o pkg/obcs:
2812     change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
2813     (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
2814     in Interior region. No impact on solution but affects Velocity monitor stats.
2815 heimbach 1.1402 o pkg/ptracers (adjoint)
2816 jmc 1.1403 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
2817 heimbach 1.1402 tape file for each tracer
2818 jmc 1.1403 o model/inc/src and pkg/autodiff: add parameters that allow to turn
2819     of parts of the adjoint code at run time. For now, there are only
2820     useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
2821     parameters are set in data.pkg.
2822     This is the lazy coward's version of doing this, but still useful for
2823     debugging. In order to do it right, everything needs to be moved to
2824 mlosch 1.1401 pkg/autodiff.
2825 jmc 1.1403 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
2826 mlosch 1.1401 the end; this fixes the adjoint balancing code for open boundaries.
2827 mlosch 1.1399 o pkg/ctrl:
2828     - change behavior of xx_${varname}period to be analogous to exf-conventions:
2829     xx_${varname}period = 0., means time-independent control part
2830 jmc 1.1403 xx_${varname}period = -12., means one-year-periodic monthly control part
2831 mlosch 1.1399 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
2832     clean up ctrl_init a little, remove unused variables
2833 mlosch 1.1400 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
2834 mlosch 1.1399 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
2835    
2836 mlosch 1.1398 checkpoint62u (2011/03/15)
2837 jmc 1.1397 o model/src:
2838     - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
2839     h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
2840     - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
2841     INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
2842     o pkg/ctrl/obcs/ecco:
2843 mlosch 1.1396 - remove obsolete, unused, and partially broken code:
2844 jmc 1.1397 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
2845 mlosch 1.1396 ALLOW_CTRL_OBCS_BALANCE
2846 jmc 1.1397 - put a stop statement into ecco/cost_obcsvol.F, but also add
2847 mlosch 1.1396 cost_obcsvol to ecco_ad_diff.list
2848 mlosch 1.1395 o pkg/ecco: fix counting cost function contributions for obcs (code
2849     by Matt M.) and diffkr for diagnostics
2850 heimbach 1.1394 o pkg/ecco, pkg/ctrl, pkg/grdchk:
2851     add cost penalty terms for initial uvel, vvel, eta controls
2852     and I/O for prior error files
2853 jmc 1.1393 o pkg/mdsio:
2854     move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
2855     (new argument) to check for tiled file in mdsioLocalDir : this fix the
2856     restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
2857 mlosch 1.1392 o pkg/ctrl:
2858     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
2859     ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
2860     unused and superfluous variables
2861     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
2862 mlosch 1.1391 o pkg/ecco
2863     - enable adjoint of Stevens OB
2864 jmc 1.1393 o pkg/ctrl/ecco/grdchk:
2865 mlosch 1.1390 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
2866 mlosch 1.1391 Fortunately, we do not have any tests for the numerous cpp-flagged
2867 mlosch 1.1390 option of "obcs as control parameters" so we will never know
2868     if this is an improvement (but at least now things compile).
2869     - remove an obsolete initialization from ecco_cost_init_barfiles.F
2870 jmc 1.1393 - fix some problems within never used ifdefs to make the code compile
2871 jmc 1.1388 o pkg/obcs:
2872     - Refine Interior mask definition to work with more complex OB (e.g.
2873     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
2874     read in Interior mask from file. Check if Interior mask is consistent
2875     with OB list of indices.
2876 heimbach 1.1387 o pkg/seaice
2877     - beginning code for a seaice tracer package,
2878     but currently only used for seaice age: SEAICE_AGE
2879     SEAICE_num = 4
2880     iTracer = 1: area-weighted ice age
2881     = 2: volume-weighted ice age
2882     = 3, 4: template for one-year vs. multi-year ice
2883     data.seaice has new namelist SEAICE_PARM03 for arrays related to
2884     SEAICE_num
2885    
2886 heimbach 1.1386 checkpoint62t (2011/03/05)
2887 jmc 1.1383 o pkg/obcs:
2888 jmc 1.1384 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
2889     then normal component. This ensures that the normal component is set
2890     correctly even when it conficts with tangential setting from an other OB.
2891     Affects results of test-experiment seaice_obcs: update the output.txt
2892     o pkg/obcs:
2893 jmc 1.1383 - add code to monitor statistics of dynamical fields at OB.
2894     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
2895     - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
2896     - change default: balance the Net inflow through all OB (instead of balancing
2897     each OB separately); keep the old method if setting OBC_balanceFacX < 0.
2898     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
2899     to match Nortern OB inflow (OBCS_balanceFacN=0).
2900 dimitri 1.1382 o pkg/seaice:
2901     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2902 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.113):
2903     - reverting seaice_growth to v 1.111 in order to have code with exact bit
2904     compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
2905     CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
2906     runtime flag SEAICEareaFormula is kept but is inactive
2907 jmc 1.1380 o model/src:
2908     - add new param to scale curvilinear grid distance and area when using
2909     a different sphere radius from the grid-files.
2910     - test/check multi-threads EXCH applied to local variable (cg2d_x)
2911 heimbach 1.1385 o adjoint:
2912     - enable adjoint of Stevens OB
2913     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
2914     (a bit delicate because of potentially modified adj. common block structure;
2915     current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
2916 jmc 1.1380
2917 jmc 1.1379 checkpoint62s (2011/02/15)
2918 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.112):
2919 gforget 1.1378 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
2920 jmc 1.1379 computing the ice cover tendency from effective thickness tendencies. Include
2921     Ian Fenty's formula.
2922     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
2923     SEAICEareaFormula.
2924 gforget 1.1378 - simplify notations for the various d_HEFF/d_AREA terms.
2925 jmc 1.1377 o pkg/gmredi:
2926     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
2927     from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
2928     add a verification test-run (front_relax.bvp) to test GM_useBVP.
2929 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.111):
2930 gforget 1.1376 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
2931 jmc 1.1379 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
2932     also melt ice.
2933 jmc 1.1377 o pkg/seaice:
2934 gforget 1.1375 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
2935     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
2936 jmc 1.1374 o pkg/cheapaml:
2937     - from Nico Wienders: New version of this package.
2938 jmc 1.1372 o pkg/flt:
2939     - add CPP options to prevent floats to re-enter the opposite side of
2940     a periodic domain (default: keep periodicity)
2941 jmc 1.1370 o pkg/gmredi:
2942     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
2943     (needed for multi-dim advection).
2944 jmc 1.1371 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
2945 jmc 1.1370 o model/src:
2946     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
2947 heimbach 1.1373 o tutorial_tracer_adjsens
2948     - extend to NLFS and replace maskC by hFacC
2949     (change reference output accordingly)
2950 jmc 1.1370
2951 jmc 1.1369 checkpoint62r (2011/01/24)
2952 jmc 1.1368 o testreport:
2953     - add option -deloutp (-do) to remove output file after successful run
2954     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
2955     extract exact list of procs from this file ; adjust COMMAND by
2956     replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
2957 mlosch 1.1367 o pkg/ecco: replace old ineffective way of penalizing deviations from
2958     first guess (of obcs) with code by Matt Mazloff
2959 jmc 1.1368 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
2960 mlosch 1.1366 exf/cal
2961     - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
2962     and handle case of obcs?period == 0
2963     Not affected by these changes: There is still an inconsistency in
2964 jmc 1.1368 the computation of start/endrec for the obcs variables for ALLOW_CAL
2965 mlosch 1.1366 defined (see comment by Menemenlis, 7-Mar-2003)
2966     - make S/R ctrl_get_gen_rec return something meaningful even if
2967     ALLOW_CAL is not defined
2968 jmc 1.1368 - ctrl_getobcs?: simplify code so that it does not need to use
2969 mlosch 1.1366 S/R exf_swapfields
2970 jmc 1.1365 o testreport:
2971     allow to test MPI with different number of processors for each experiment:
2972     create file "SIZE.h.mpi" in each build dir.
2973     Note: update of "-command" argument not yet implemented.
2974 gforget 1.1364 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
2975     alleviate the need for additional 3D tapes when using
2976     the non-inear free surface in the adjoint. This is done
2977 jmc 1.1368 by adding an 'update' of hfacc etc. to their current
2978     value at the beginning of forward_step.F.
2979 mlosch 1.1362 o pkg/seaice
2980     seaice_lsr: move stress-divergence computations out of outer pseudo-
2981 jmc 1.1363 timestepping loop
2982 mlosch 1.1362 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
2983     up, so that the calls of the ctrl_* subroutines are really at the end
2984     of the routine.
2985 jmc 1.1363 o pkg/gmredi:
2986     allow to specify a 2-D horizontal map and a 1-D vertical profil
2987     as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
2988 gforget 1.1364 o pkg/seaice:
2989     move lsr iterations from seaice_dynsolver to seaice_lsr.
2990     o pkg/seaice:
2991     reduce memory footprint of seaice mutldim advection tapes,
2992     by using a 2D tape independent of the generic_advdiff ones,
2993     and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
2994 mlosch 1.1362
2995 jmc 1.1361 checkpoint62q (2010/12/29)
2996 jmc 1.1360 o model/src:
2997     - check horizontal grid-spacing for unset or zero/negative values.
2998     - change AD test hs94.1x64x5 to be truly a 2-D set-up.
2999 jmc 1.1359 o pkg/flt:
3000     - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
3001     - precision of input and output files set according to readBinaryPrec
3002     and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
3003     - initial float position from tiled file was not converted to index space
3004     (looks like a bug): fixed to make it similar to initial pos. global file.
3005 jmc 1.1358 o global_ocean.cs32x15:
3006     change SIZE.h of AD set-up to get same tiling as with MPI.
3007     Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
3008     o model/src:
3009     add flag to control printing of domain fields (bathymetry, hFac ...) in
3010     ini_mask_etc (call to plot_fieds_xy*).
3011     o pkg/thsice:
3012     if useEXF, some forcing fields are not valid in overlap: fixed by computing
3013     over the interior only + apply EXCH at the end (like with SEAICE advection).
3014 jmc 1.1357 o pkg/mdsio:
3015     - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
3016     to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
3017     - change barrier call for safe multi-threads access to 3-D shared buffer.
3018     - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
3019     - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
3020     remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
3021 jahn 1.1356 o pkg/flt:
3022     - add fourth-order Runge-Kutta integration
3023     - add basic exch2 support (only 1 facet supported so far!)
3024 jmc 1.1355 o pkg/mdsio+rw:
3025     new S/R to read local (or tile independent) vector (read counterpart of
3026     mds_writevec_loc, and front-end write_glvec_rl/rs).
3027 gforget 1.1354 o global_ocean.cs32x15: additional input_ad.seaice experiment
3028     that uses pkg/seaice rather than pkg/thsice.
3029     (using multidim advection for seaice)
3030 jmc 1.1353 o towards more F95 syntax for array specification in namelist:
3031     - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
3032     of all verification experiments.
3033     e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
3034     was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
3035     - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
3036 gforget 1.1352 o global_ocean.cs32x15: additional input.seaice experiment
3037     that uses pkg/seaice rather than pkg/thsice.
3038 jmc 1.1353
3039 jmc 1.1350 checkpoint62p (2010/12/17)
3040 gforget 1.1351 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
3041     to THSICE_SIZE.h to avoid conflict with pkg/seaice.
3042     o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
3043     allow for use of multim. advection in seaice adjoint.
3044 mlosch 1.1349 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
3045     - first attempt to close budgets by taking into account the freshwater
3046 jmc 1.1350 flux implied by the sublimation of snow and ice. So far only the
3047 mlosch 1.1349 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
3048     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
3049 jmc 1.1348 o eesupp/src:
3050     new S/R with new option (NML_EXTENDED_F77) to change array specification
3051     from F95 standard to commonly accepted extended F77 form.
3052     This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
3053     and to revert back to the original syntax (with -DNML_EXTENDED_F77)
3054     for less tolerant f77 compiler (e.g., pgf77, g77).
3055 jmc 1.1346 o globalFiles:
3056     commented out in parameter file "data" since it's not safe with MPI
3057     (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
3058     in this case); no longer commented out in restart test (tst_2+2).
3059     o add adTapeDir to specify a special directory where adjoint tapes are
3060     written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
3061 mlosch 1.1345 and cannot be used together with mdsioLocalDir.
3062 jmc 1.1343 o nesting pkgs:
3063     - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
3064     - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3065     - add parameter files + utils dir + output from short run on beagle.
3066 gforget 1.1344 o pkg/seaice:
3067     fix seaice_growth.F store directives; update results of exp. lab_sea.ad
3068 jmc 1.1343 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
3069 mlosch 1.1342 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
3070    
3071 jmc 1.1341 checkpoint62o (2010/11/25)
3072 jmc 1.1340 o pkg/exf:
3073     - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
3074 jmc 1.1341 o pkg/seaice:
3075     - seaice_ocean_stress: split a loop for better vectorization of the
3076     adjoint code
3077 mlosch 1.1337 - seaice_growth.F: fix bug in conservation of freshwater connected to
3078 mlosch 1.1338 capping of heff, put contribution into d_HEFFbyNEG
3079 mlosch 1.1337 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
3080     by something more sensible (parameters that are what their name implies)
3081     - change some defaults, so that by default exf-parameters are used for
3082     things like rhoAir, cpAir,latent/sensible heat parameters, in order
3083     to reproduce the old results, many data.seaice now contain funny values
3084     for cpAir and latent heat of sublimation
3085 jmc 1.1341 o packages_readparms.F: move exf_readparms up in line so that
3086 mlosch 1.1337 exf-parameters are visible for other packages (e.g. seaice)
3087 jmc 1.1336 o debugMode & debugLevel=2:
3088     - differentiate between debugMode & debugLevel=2:
3089     debugMode: controls printing of debug messages (sequence of S/R calls).
3090     debugLevel: controls printing of algorithm intermediate results and stats.
3091     - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
3092     => allows to print debug-stats without all sequence of call messages.
3093     - switch control of debug print from debugLevel to debugMode in many S/R.
3094     o pkg/obcs (obcs-sponge):
3095     fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
3096     call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
3097 jmc 1.1335 o pkg/generic_advdiff:
3098     - record overlap minimum size for each advection scheme;
3099     - refine criteria on overlap minimum size;
3100     - check and stop (in gad_check) if overlap size is too small.
3101     o pkg/obcs:
3102     - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
3103     once, in ptracers_implicit.F)
3104     - with seaice: remove test on empty file name in obcs_apply_seaice (always
3105     apply OB values when tile has OB)
3106 jmc 1.1334 o model/src, coriolis setting:
3107     - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
3108     useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
3109     files (selectCoriMap=3) with any grid.
3110     - add parameter "fPrime" for constant second Coriolis coeff (default=0).
3111     o pkg/seaice/seaice_growth.F:
3112     a few cosmetic changes that reduce the number of lines of code
3113 mlosch 1.1332 o pkg/obcs: add boundary conditions following Stevens (1990)
3114     - the code follows old MOM/NAOSIM code
3115     - so far it is only implemented for the eastern and western boundaries
3116     and NOT for pTracers
3117 jahn 1.1331 o pkg/rbcs:
3118     - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
3119     beginning of the first rbcs forcing period.
3120     - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
3121     offline package, i.e., one file per time, labeled by iteration number;
3122     deltaTrbcs sets the timestep with which the data was generated;
3123     rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
3124     - rbcsForcingCycle=0 makes forcing non-cyclic.
3125     - make arithmetic safe for negative times and odd forcing periods.
3126    
3127 jmc 1.1330 checkpoint62n (2010/11/09)
3128 mlosch 1.1327 o pkg/seaice:
3129 jmc 1.1329 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
3130     o pkg/obcs:
3131     New S/R to copy tracer value from the OB location to narrow band region
3132     (width = same as overlap) beyond the OB: preserve OB value (needed for
3133     high-order scheme) which were overwritten by EXCH call if in overlap
3134     region. Applied to theta, salt, ptracer and advected seaice variables.
3135     With seaice: use maskInC in similar way as in gad_advection.F,
3136     in seaice_advection.F and advect.F.
3137     Update output of experiment seaice_obcs and change exp4 to test OBCS with
3138     4th order Adv.Scheme. for pasive salt and ptracer.
3139     o tools/genmake2:
3140     - when looking for an optfile (not specified), only search for Fortran compiler
3141     (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
3142     - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
3143     (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
3144     - set default for CPP to "cpp -traditional -P" (was the case without specifying
3145     an optfile, but otherwise default was just "cpp".
3146     - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
3147     - when "CC" is not set in the optfile, look for possible C compiler
3148     (instead of just setting CC=cc)
3149     - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
3150     => add a ".F" to ".o" rule for source files with no "#include" (such as
3151     port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
3152     - move gfortran before g77 in list of possible Fortran compiler (consistent
3153     with reference compiler switch from g77 to gfortran)
3154     o pkg/seaice:
3155     o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
3156 mlosch 1.1327 seaice_check that stops the model, when the CPP flag is used.
3157     o seaice_growth.F: make capping of ice volume conserving by returning the
3158     capped ice as freshwater to EmPmR. This does not change the verification
3159     experiments but will change runs where the capping is acutally active
3160 jmc 1.1326 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
3161     (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
3162     global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
3163     lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
3164     o tools/genmake2:
3165     - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
3166     - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
3167     - clean previous genmake log files before anything else.
3168     - change Makefile to remove testreport log files (*.tr_log) and genmake log
3169     files only with "CLEAN" target (instead of "Clean");
3170 jmc 1.1324 o pkg/generic_advdiff:
3171     Change OBCS in multiDim advection (gad_advection.F):
3172     Use maskInC to prevent intermediate update of tracer-field in OB regions,
3173     thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
3174     which were applying future time-step OB values.
3175     This way, all explicit calculations use current-time-step OB values
3176     (simpler and more consistent).
3177     Affects results when set-up uses time-varying OBC and multi-dim advection;
3178     update output of experiment seaice_obcs.
3179 jmc 1.1323 o pkg/seaice:
3180     move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
3181     this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
3182     SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
3183     Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
3184     but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
3185     unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
3186 dfer 1.1322 o pkg aim (2010/10/26):
3187     - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
3188     formulation with obliquity, eccentricity, ... as run-time parameters,
3189     - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
3190     upward shortwave radition at the surface (all-sky and clear-sky).
3191 jmc 1.1319 o pkg/obcs:
3192 dimitri 1.1321 - writing sections with globalFiles=T does not work: switch to tiled-files
3193     when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
3194     - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
3195     - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
3196 jmc 1.1319
3197 jmc 1.1318 checkpoint62m (2010/10/21)
3198 mlosch 1.1316 o pkg/seaice: vectorize seaice_solve4temp.F
3199     - move iterations loops outside of i/j-loops
3200     - requires 2D arrays for TB and effConduct
3201 jmc 1.1318 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
3202 mlosch 1.1316 modified in this routine
3203     - a little bit of clean up, adjusting indentation, etc.
3204 jmc 1.1318 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
3205     performance and '**TWO' by '**2' (because TWO is a float),
3206 mlosch 1.1316 replaced ONE, ZERO
3207 jmc 1.1314 o eesupp/src:
3208     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
3209 gforget 1.1313 o pkg/seaice/seaice_growth.F
3210 jmc 1.1314 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
3211     merging process. The merged routine has two branches, and one activates the 'evolution'
3212 gforget 1.1313 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
3213     In summary, here is what the '10/10 revision' did consist of
3214 jmc 1.1314 part 1: seaice_growth.F revisions 1.71 to 1.75
3215 gforget 1.1313 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
3216 jmc 1.1314 The emphasis here was on improving readability (e.g. by trying to use meaningful
3217 gforget 1.1313 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
3218 jmc 1.1314 part 1.5:
3219     - revising the lab_sea experiment to make it a more useful (i.e. stable
3220     and representative of an actual model run). This was done by generating a
3221     (winter) pickup to start from, switching back the main experiment dynamic
3222 gforget 1.1313 solver from evp to lsr, having one of the experiments use the free drift solution.
3223 jmc 1.1314 part 2: seaice_growth.F revisions 1.76 to 1.85
3224 gforget 1.1313 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
3225 jmc 1.1314 - Sorting out the various fields units and sign (set early on and reset at the end)
3226     to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
3227     fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
3228     - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
3229 gforget 1.1313 and simplifying logical expressions to further improve readibility.
3230     part 3: seaice_growth.F revisions 1.86 to 1.89
3231     - Re-organize the blocks of code more logically.
3232     - Merging the '_if.F' pieces that add something new.
3233 jmc 1.1314 o pkg/thsice:
3234     - vectorize thsice_solve4temp and thsice_get_exf.
3235 mlosch 1.1312 Problem: thsice_solve4temp has an unvectorizable statement that
3236     might also be problematic for TAF
3237 jmc 1.1314 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
3238     does not change the verifcation experiment, but will change all
3239 mlosch 1.1312 experiments that have this flag undefined (not tested in verification);
3240     a little reorganization to save a few 2D fields and recomputations
3241 heimbach 1.1315 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
3242 heimbach 1.1317 - 2nd step: fix some store dirs
3243     o seems to work somewhat, i.e. using ifort but not g77
3244     o likely cause are incomplete init. or recomputation
3245     o start verification/global_ocean.cs32x15/input_ad.thsice
3246 jahn 1.1311 o pkg/obcs: add support for exch2
3247     - the position of the boundary and prescribed values are specified using
3248     a global domain with exch2 facets stacked
3249     - in x for N,S boundaries (like W2_mapIO=-1)
3250     - in y for E,W boundaries (so E,W boundaries do not overlap)
3251     o pkg/mdsio: add support for writing global sections with exch2
3252     file layout is as for obcs described above:
3253     - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
3254     - for y-z sections, facets are stacked in y
3255 jmc 1.1309 o pkg/thsice:
3256 mlosch 1.1310 - change a few routines for better vectorization: thsice_albedo.F,
3257     thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
3258     not affected, but in particular the latter routine has changed
3259     dramatically (not necessarily easier to read now).
3260     - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
3261 jmc 1.1309 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
3262 gforget 1.1308 o verification/lab_sea:
3263     - overhaul of the forward model experiments. The main motivation
3264 jmc 1.1314 for this revision is that lab_sea has proven quite fragile (when
3265 gforget 1.1308 changing the sea-ice code, and switching platforms) to a point
3266     when failures were very hard to attribute to specific code problems.
3267 jmc 1.1314 - the suspected reason for this fragility is noise amplification by evp so,
3268 gforget 1.1308 to start with, we decided to replace evp with lsr in the main experiment.
3269     - the input.lsr experiment thus became obsolete and was removed.
3270 jmc 1.1314 - it was replaced with the input.fd experiment that uses an
3271 gforget 1.1308 analytical "free drift" solution as the ice velocity field.
3272     - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
3273     will hopefully allow us to discriminate problems due to dynamic solvers
3274     from problems due to the thermodynamic code. input.salt_plume (lsr) allows
3275     us to test additional options, along with the salt plume package.
3276 jmc 1.1314 - Finally a pickup was generated (at the end of a one year run) to
3277 gforget 1.1308 make the tests more representative of an actual model run. Previously
3278     the tests starting point was a 1m thickness of ice everywhere.
3279 jmc 1.1314 o pkg/seaice:
3280 gforget 1.1308 - introducing S\R seaice_freedrift.F that compute the
3281 jmc 1.1314 analytical solution to an approximate ice momentum
3282 gforget 1.1308 equation (i.e. the simple stress/coriolis balance).
3283     - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
3284 jmc 1.1314 of the free drift velocity field, and enable its use.
3285     To actually use the free drift solution as the model ice
3286     velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
3287 mlosch 1.1307 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
3288    
3289 jmc 1.1306 checkpoint62l (2010/10/04)
3290 jmc 1.1305 o pkg/seaice:
3291     -fix the USE_ORIGINAL_SBI version (for variable freezing point);
3292     -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
3293     version (with USE_ORIGINAL_SBI undef);
3294 mlosch 1.1304 o add hooks for new packages OASIS, the package will follow
3295     (hooks exclude the seaice pkg for now)
3296 gforget 1.1303 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
3297 jmc 1.1305 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
3298 gforget 1.1303 rather than mdsio_readvector.F/mdsio_writevector.F, within
3299     adread_adwrite.F to read/write adjoint-related tapes to disk.
3300 jmc 1.1305 o eesupp and pkg/mdsio: ALLOW_WHIO
3301     Option to write/read 2D fields to files including tiles halos.
3302     The main purpose is for adjoint related "tape I/O".
3303 gforget 1.1302 The secondary purpose is for debugging phases.
3304     A word on those rather specifically intended purposes.
3305     The code was meant to be stripped down to the bare minimum.
3306 jmc 1.1305 Typically, there is a unique and basic mapping to the global
3307 gforget 1.1302 buffer (tile by tile, then proc by proc, then level by level), and
3308     byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
3309 jmc 1.1305 meant to generate user friendly outputs of various shapes and forms.
3310 gforget 1.1302 Rather it is intended, for the knowledgeabale developers,
3311     to be largely independent of the many mdsio options, to allow
3312 jmc 1.1305 outputs of tiles+halos in debugging phases and in adjoint runs,
3313 gforget 1.1302 and to allow some flexibility in tuning (adoint) I/O depending on each
3314 jmc 1.1305 file system behavior. With regard to tuning, most of the potential knobs
3315 gforget 1.1302 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
3316     to specify directories, to specify the typical size of I/O calls, etc.)
3317     are not yet included, and will be added if they prove useful.
3318 jmc 1.1300 o pkg/seaice:
3319 jmc 1.1301 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
3320     o pkg/seaice:
3321 jmc 1.1300 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
3322     code (seaice_budget_ice_if.F) which enable to recover old standard
3323     code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
3324     temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
3325     o model/src (rStar):
3326     use simple average (not area weighted) of rStarFac at U,V point when using
3327     vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
3328     update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
3329 jmc 1.1299
3330 jmc 1.1298 checkpoint62k (2010/09/17)
3331 heimbach 1.1297 o adjoint
3332     * changed verification/global_ocean.cs32x15 ; adjoint now tests
3333     Adams-Bashforth 3 + NLFS + RSTAR
3334     * some more modifs required for ECCO-GODAE v4
3335 dimitri 1.1296 o pkg/seaice
3336     add SEAICE_AGE_VOL option to use volume instead of area for
3337     integrating SEAICE_AGE
3338 jmc 1.1295 o model/src:
3339     first check-in of sigma & hybrid-sigma coordinate code ; also includes
3340     non-linear free-surface parts ; but pressure-gradient not yet coded.
3341 jmc 1.1294 o pkg/ptracers:
3342     option for ptracer to convert Salt Relax into additional EmP.
3343     tested in exp. global_ocean.90x40x15.dwnslp (update output)
3344    
3345 jmc 1.1293 checkpoint62j (2010/08/25)
3346 jmc 1.1292 o pkg/ggl90:
3347     other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
3348 mlosch 1.1291 o pkg/dic: car_flux.F, phos_flux.F
3349     - reduce number of exp-calls in order to improve performance
3350 jmc 1.1292 - clean up a little (replace fields by their macros, etc., fix
3351 mlosch 1.1291 typo in CPP-flag)
3352 gforget 1.1290 o pkg/ggl90: minor changes
3353     - GGL90diffKrS was removed --> always use GGL90diffKr
3354     - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
3355 jmc 1.1292 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
3356     (commented out for now)
3357 gforget 1.1290 - change in max/min operations to ensure that smoothing is ok
3358     - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
3359     - always use diffKrNrT as background profile (i.e. never use diffKr field)
3360 mlosch 1.1289 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
3361 mlosch 1.1286 o pkg/dic:
3362 mlosch 1.1288 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
3363     vectorization
3364 mlosch 1.1287 - small bug fix in insol for the unlikely case of a cartesian grid
3365     - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
3366     + now vectorize, which also removes adjoint recomputations;
3367     + replace integer maksp1 by _RL maskp1
3368 mlosch 1.1288 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
3369 mlosch 1.1286
3370 jmc 1.1285 checkpoint62i (2010/07/21)
3371 jmc 1.1284 o pkg/flt:
3372     - with OBCS: stop floats which enter the OB region
3373     o model/src:
3374     - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
3375     for implicit vertical advection.
3376 jmc 1.1283 o pkg/seaice:
3377     - account for melting in seaice age evolution.
3378 jmc 1.1284 - remove double counting of seaice ridging effect on seaice age.
3379 jmc 1.1283
3380 jmc 1.1282 checkpoint62h (2010/06/18)
3381 jmc 1.1281 o pkg/exch2:
3382     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
3383     o tools/genmake2
3384     - remove "-pdefault" option: redundant with the use of "packages.conf";
3385     - remove file pkg/pkg_default : set the default as a pkg group
3386     ("default_pkg_list") defined in pkg/pkg_groups;
3387     - fix for case pkg/pkg_depend is missing (was hanging before);
3388     - add option "-pgroups" to specify a different pkg_groups than the default.
3389 jmc 1.1280 o verification/adjustment.cs-32x32x1:
3390     add a "minimal" set-up test (code_min & input_min) which only compiles
3391     eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
3392 jmc 1.1279 o tools/genmake2
3393     - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
3394     - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
3395 mlosch 1.1277 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
3396     files are nearly the same anyway.
3397     Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
3398     - redefinition of tau(i,i) (by a factor of ustar)
3399     - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
3400     - replace rhonil by rhoConstFresh in computation of evap (bug fix)
3401     - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
3402 jmc 1.1278 - replace
3403 mlosch 1.1277 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
3404     shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
3405     by
3406     shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
3407     (changes results)
3408 jmc 1.1278 -> exf_bulkformulae v1.22,
3409 mlosch 1.1277 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
3410     (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
3411 jmc 1.1278 output.txt 1.63
3412 mlosch 1.1277 offline_exf_seaice: output.seaicetd.txt 1.7
3413     seaice_obcs: output.txt 1.10)
3414     Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
3415     -> exf_bulkformulae v1.23,
3416     unfortunately requires updating lab_sea.salt_plume (6 matching digits),
3417     and global_ocean.cs32x15.icedyn (only 11 matching digits)
3418 jmc 1.1278 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
3419 jmc 1.1276 o adjoint of exch-1:
3420     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
3421     (note: was already like this when using EXCH-2) and remove flow dir
3422     and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
3423     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
3424     - update pkg/exch2 diff list.
3425    
3426 jmc 1.1275 checkpoint62g (2010/05/19)
3427 jmc 1.1274 o eesupp/src (exch-1):
3428     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
3429     and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
3430     (renamed to exch1_*rx_cube.F).
3431     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
3432     to call new exch1 S/R ; update Makefile and .cvsignore.
3433     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
3434     exch2_xy_rx later)
3435     Note: after updating your code, need to run "make clean" in eesupp/src
3436 jmc 1.1273 o test experiment bottom_ctrl_5x5:
3437 jmc 1.1274 new output_adm.txt with fewer grdchk & less monitor output.
3438 jmc 1.1273 o model/src:
3439     remove the call to ini_cori in initialise_varia.F (just keep the usual one
3440 jmc 1.1274 in initialise_fixed.F). More consistent with coriolis & horizontal grid
3441 jmc 1.1273 beeing treated in the same way (ini_grid is not called a 2nd time).
3442 jmc 1.1274 o pkg/exf:
3443 mlosch 1.1272 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
3444 mlosch 1.1271 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
3445 mlosch 1.1272 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
3446     - cosmetic changes to exf_bulkformulae.F to make it look more like
3447     exf_bulk_largeyeager04.F
3448 jmc 1.1270 o eesupp/src (exch-1):
3449     - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
3450     - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
3451     array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
3452     (even without using MPI).
3453     - Message mode: move RecvAck setting (indicator of buffer being ready)
3454     from send_put to recv_get S/R (was useless before, but not sure if
3455     it's much more useful now);
3456 jmc 1.1273 - Switch the order of sync: MPI-proc 1rst and then threads;
3457 jmc 1.1270 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
3458 jmc 1.1273 - fix AD code for communication mode ='get' (but not used).
3459 jmc 1.1269 o model/src:
3460     initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
3461     not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
3462 mlosch 1.1268 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
3463 mlosch 1.1267 o pkg/ctrl: require a specific set of control variables and exf-flags for
3464     adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
3465 gforget 1.1264 o model/src:
3466 jmc 1.1266 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
3467     1rst forward sweep, to avoid over-writing output files during recomputations
3468     recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
3469     b) 2nd version:
3470     - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
3471     - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
3472     writePickupAtEnd) + seaice & ptracers output;
3473     - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
3474 jmc 1.1265 o model/src:
3475 gforget 1.1264 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
3476 jmc 1.1263 o pkg/exch2:
3477 jmc 1.1265 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
3478 jmc 1.1263 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
3479 jmc 1.1262 o pkg/autodiff & exch2:
3480     process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
3481     (for now, only if ALLOW_EXCH2 is defined).
3482 jmc 1.1261 o pkg/autodiff:
3483 jmc 1.1265 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
3484 jmc 1.1261 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
3485     + clean-up comments (_RS is not always real*4)
3486     - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
3487     - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
3488     was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
3489 jmc 1.1260 o testreport (AD-tests):
3490     no longer link files from dir "../input" (1rst link files from
3491     "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
3492    
3493 jmc 1.1259 checkpoint62f (2010/04/29)
3494 mlosch 1.1258 o model/src/the_main_loop.F:
3495     adjust store directives for seaice evp and multicategory according to
3496     pkg/ecco/the_main_loop.F
3497 heimbach 1.1256 o adjoint:
3498 jmc 1.1260 global_sum_ad was incomplete (noted many times by many people ;)
3499 heimbach 1.1256 nice description by Jean U. as follows:
3500 jmc 1.1260 * allreduce(var) in global_sum.F can be interpreted as
3501     reduce(sum) followed by broadcast of sum.
3502     * The adjoint of that is
3503     sum(adjoint) followed by broadcast(summed adjoint value)
3504 heimbach 1.1256 or in other words, allreduce(sum, adjoint vars)
3505     We were missing the sum(adjoint)!
3506     Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
3507     (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
3508     The fix should produce 16-digit accuracy between
3509     single-CPU multi-tile (e.g. nSx=2, nPx=1) and
3510     multi-CPU single-tile (e.g. nSx=1, nPx-2)
3511     We'll probably change this yet again shortly
3512 jmc 1.1257 o eesupp/src:
3513     - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
3514 dimitri 1.1255 o pkg/icefront
3515     - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
3516     specification of addmass array based on a 2D field, which is added
3517     at bottommost wet level at each horizontal location.
3518 jmc 1.1254 o model/src:
3519     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
3520     layout; (not always compatible with delX,delY setting; commented out for now).
3521 jmc 1.1253 o pkg/exch2:
3522     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
3523     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
3524    
3525 jmc 1.1252 checkpoint62e (2010/04/15)
3526 jmc 1.1251 o pkg/obcs:
3527     - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
3528 jmc 1.1250 o pkg/dic:
3529     -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
3530     (note: not presently tested in any forward verification exp.)
3531     update tutorial_global_oce_biogeo AD output file.
3532     o pkg/exf:
3533 gforget 1.1249 - account for the variation of albedo as a function of zenith angle
3534 jmc 1.1250 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
3535 jmc 1.1248 o build_options:
3536     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
3537     o pkg/dic:
3538     change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
3539     - use binary pickup file for restart;
3540     - initialise atmos-CO2 box from dic_pCO2 parameter;
3541     - fix multi-threaded.
3542 jmc 1.1247 o pkg/rbcs:
3543     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
3544     change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
3545     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
3546     and update output.txt
3547 jmc 1.1246 o pkg/kpp:
3548     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
3549     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
3550 jmc 1.1248 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
3551 jmc 1.1246 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
3552     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
3553     KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
3554 dfer 1.1244 o pkg/offline:
3555 jmc 1.1245 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
3556     (bug was added in version 1.10 on 2007-08-23).
3557     o pkg/offline:
3558 dfer 1.1244 - no need to specify periodicExternalForcing, etc ... to use offline pack
3559     - offline input files no longer just single prec --> parameter offlineLoadPrec
3560 heimbach 1.1242 o verification/lab_sea:
3561 jmc 1.1245 change AD test to multi-tile setup and update all 4 AD output.
3562 heimbach 1.1242 NOTE: while cost function values remain very similar,
3563     gradients are very different, although gradient checks are self-consistent
3564     Should try to get to the bottom of this (cost function summation order?)
3565 jmc 1.1241 o pkg/dic:
3566     in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
3567     a weakness of TAF that drops part of double precision in log10 derivative.
3568 jmc 1.1243 <= changes removed since problem has been fixed in current TAF version 1.9.71
3569 jmc 1.1241 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
3570 jmc 1.1240 o pkg/ecco:
3571     add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
3572     update all 4 lab_sea AD output.
3573    
3574 jmc 1.1239 checkpoint62d (2010/03/22)
3575     o build_options:
3576     remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
3577 jmc 1.1238 o remove unbalanced quote (single or double) in commented line of source code
3578     (may cause some warning with some preprocessor/makedepend versions).
3579     o pkg/seaice:
3580 jmc 1.1237 fix seaice_model.F for adjoint (gael) and update AD results of experiments
3581     lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
3582 jmc 1.1236 o testreport:
3583     add option '-runonly' (short: '-ro') to just do the run part (without make).
3584 jmc 1.1235 o eesupp: remove JAM communication code (obsolete).
3585 jmc 1.1234 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
3586     (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
3587     to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
3588     (update also the output).
3589    
3590 jmc 1.1233 checkpoint62c (2010/03/02)
3591 jmc 1.1232 o tools/build_options :
3592     move (some) old optfiles from build_options/ to build_options/unsupported/
3593 gforget 1.1231 o model/src and pkg/exf
3594     surface relaxation -- separating data and data.exf options
3595     The point is to ensure that we specify the surface relaxation
3596     either in data or in data.exf (but not half and half) and to
3597     avoid an accidental relaxation to 0 (which happened if a time
3598     scale was specified but the file name was left empty)
3599 gforget 1.1230 o model/src model/inc and pkg/mom_common
3600     ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
3601     => addition to the viscosity field as computed by others schemes
3602 jmc 1.1229 o tools/build_options:
3603     - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
3604     but keep the former optfile for few weeks for smooth transition
3605 gforget 1.1228 o pkg/ecco
3606     - allow user defined cost function contributions
3607 dfer 1.1322 CPP: ALLOW_USERCOST_CONTRIBUTION
3608     USAGE: compute contributions in cost_usercost_all.F
3609 gforget 1.1228 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
3610     the two options are complementary.
3611 gforget 1.1227 o pkg/smooth
3612     - migration from contrib to the main repository
3613 jmc 1.1229
3614 jmc 1.1226 checkpoint62b (2010/01/26)
3615 jmc 1.1225 o pkg/monitor:
3616     - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
3617     (in case someone forgot to update customized pieces of code)
3618     o nonHydrostatic:
3619 jmc 1.1224 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
3620     - add a simple 2-D experiment (short_surf_wave) to test it.
3621     o pkg/icefront:
3622     adding the shell of, and the hooks to, a new package that
3623 dimitri 1.1223 will model melting and freezing of vertical glacier ice fronts
3624 jmc 1.1224 o momentum:
3625 jmc 1.1222 add diagnostics of momentum tendency from Hydrostatic pressure gradient
3626     (without surf.pressure term: would need a 2nd filling since implicit term).
3627 jmc 1.1224 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
3628     two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
3629     cannot deal with the former
3630 jmc 1.1220 o cleaning:
3631 jmc 1.1222 - remove all (except OpenAD) old TLM output from results_ad dirs.
3632 jmc 1.1220 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
3633     - comment out maskH definition (replaced by maskInC)
3634     o pkg/monitor:
3635     - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
3636 jmc 1.1225 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
3637 jmc 1.1220
3638 jmc 1.1219 checkpoint62a (2010/01/15)
3639 jmc 1.1218 o model/src:
3640     - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
3641 jmc 1.1217 o pkg/diagnostics:
3642     - add optional level number diagnostics (i.e., level number to be define
3643     explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
3644     - strictly check for valid parser-code(10) ;
3645     - check if adding diag to the list from the right place.
3646 jahn 1.1216 o pkg/longstep:
3647     - change parameters and fix tracer conservation with rstar/nonlinear free surface
3648 jmc 1.1215 o diagnostics:
3649     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
3650     S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
3651 jmc 1.1214 o pkg/diagnostics:
3652     - Add option for writing vertical integral (sum of selected levels) of an output
3653     field instead of writing output field levels. Activate this option on a per
3654     output-file basis, by setting the 2nd character of fileflag to 'I'.
3655     - Add field-specific information relative to level integral in 3rd postion
3656     of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
3657     vertically (x level-thickness x hFac), "r"=same but without hFac.
3658 jmc 1.1213 o do_the_model_io:
3659     - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
3660     in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
3661     writing pickups and stopping.
3662     o pkg/diagnostics (for now, only with mdsio):
3663     - write time information to meta file (and modify accordingly rdmds.m) :
3664     time-averaged diagnostics output: write starting and ending time of the
3665     time-averaging interval ; snap-shot diagnostics output remains unchanged;
3666 jmc 1.1212 o pkg/timeave:
3667     - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
3668     always Nr), now assumed to be equal to number of levels of averaged field;
3669     only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
3670     o pkg/sbo:
3671     - fix ocean bottom pressure global-average & 2-D time-ave output (was
3672     neither initialised nor filled).
3673     - add starting iteration in suffix of global-average output file
3674     (to avoid over-writing the file after a restart)
3675     - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
3676     o time-average:
3677     - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
3678     (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
3679     ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
3680     this fix DIC_COST cumulative-time array (previously: bi,bj,k)
3681     - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
3682     - fix missing accumulation for pkg/opps.
3683     - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
3684     (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
3685     - fix initialisation of time-ave vars and do only full time-step increment
3686     (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
3687 jmc 1.1211 o pkg/layers:
3688     - use standard RW pkg S/R to write the output
3689     and remove local write_fld version (which had a problem).
3690     - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
3691     - fix LAYERS_CALC argument list.
3692     o pkg/timeave:
3693     - store cumulative-time in a simple tiled array (drop the level index)
3694     - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
3695 jmc 1.1210 o pkg/ocn,aim_compon_interf
3696     - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
3697    
3698 jmc 1.1209 checkpoint62 (2009/12/23)
3699 jmc 1.1208 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
3700     (was not previously tested in any other exp.)
3701 jmc 1.1207 o pkg/monitor:
3702     - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
3703 jmc 1.1209 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
3704 jmc 1.1207 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
3705     - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
3706     - change del2 calculation.
3707     - use interior masks (instead of maskH, <- to be remove).
3708     - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
3709     o mask & obcs:
3710     - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
3711 jmc 1.1209 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
3712 jmc 1.1207 (called after packages_init_fixed)
3713 jahn 1.1206 o pkg/obcs:
3714     - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
3715     Fixes bug in obcs+exf with nSx*nSy.GT.1
3716     - fix multi-tile handling in obcs balance code
3717 jmc 1.1205 o nonHydrostatic:
3718     - Implement AB-3 for non-hydrostatic vertical momentum ;
3719     (change ordering of var. stored in pickup file when using NH)
3720     - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
3721     - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
3722     (in prep. for new NH free surface form).
3723 jmc 1.1204 o pkg/obcs:
3724     add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
3725 jmc 1.1209 o model/src:
3726 jmc 1.1204 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
3727    
3728 jmc 1.1203 checkpoint61z (2009/12/01)
3729 jmc 1.1202 o nonHydrostatic:
3730     Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
3731     a spurious source of energy in simple baroclinic adjusment test case.
3732     Update all non-hydrostatic exp output.
3733     o model/src (3-d solver):
3734     Change again 3-D solver free-surface RHS term when exactConserv=T:
3735     simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
3736     (which was not the case with previous formulation).
3737     To recover previous version, just reset "oldFreeSurfTerm" to previous value.
3738     Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
3739     o nonHydrostatic:
3740     - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
3741     for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
3742     - change 3-D solver to work with r* (for now, only with linear free-surf.)
3743     - add few debug diagnostics (cg3d_x, residual)
3744 jmc 1.1201 o model/src:
3745     fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
3746     update output of exp. global_ocean.cs32x15.viscA4
3747 jmc 1.1200 o update output of exp. global_ocean.cs32x15.icedyn after removing
3748     #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
3749     o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3750 mlosch 1.1199 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
3751     for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
3752 mlosch 1.1198 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
3753 jmc 1.1200 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
3754     runtime flag useSRCGSolver. Modify verification experiment global_with_exf
3755     to test this code
3756 jmc 1.1197 o pkg/cd_code:
3757     Change defaut D-grid time-stepping to get the same for D-grid momentum as for
3758     C-grid momentum. D-grid velocity used to be stepped forward in time with
3759     Adams-Bashforth only on surface pressure term. Tests show that using AB on
3760     D-grid coriolis term improves stability (as expected from CD-scheme paper).
3761     To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
3762     Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
3763     lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
3764     tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
3765     Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
3766 jmc 1.1204 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
3767 jmc 1.1196 o pkg/obcs:
3768 jmc 1.1197 - fix bug in initialisation (broken since Oct 1rst modification)
3769 jmc 1.1196 for useOBCSprescribe without useEXF.
3770    
3771 jmc 1.1203 checkpoint61y (2009/11/15)
3772 mlosch 1.1194 o pkg/seaice
3773     - change (once again) the discretization for the evp solver: rather than
3774     squaring the averages of strain rates, average the squares to give
3775     a better approximation to VP behavior (in simple test); this breaks
3776     verification experiments that use EVP (lab_sea and lab_sea.hb87)
3777     --> update outputs
3778 jmc 1.1195 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
3779 mlosch 1.1193 to improve vectorization of adjoint code on TARGET_NEC_SX
3780 dfer 1.1192 o verification/vermix:
3781 mlosch 1.1194 - change vermix to a more "classical" 1d column with high vertical
3782     resolution, seasonal heat flux forcing and constant wind forcing
3783     --> update outputs
3784 mlosch 1.1190 o pkg/seaice
3785     - fix diagnostics of principal stress components for EVP
3786     - add optional diagnostics of non-linear convergence for LSOR solver
3787 mlosch 1.1191 - make maximum zeta a runtime parameter
3788 jmc 1.1189 o model/src (3-d solver):
3789     Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
3790     which consisted in removing the Surf. Non-Hydrostatic pressure from the
3791     whole column and adding it to Eta (inspired from Casualli, 1999):
3792     Only affects 3-D solver initial guess and only if using ExactConserv,
3793     but tests did show a degradation of solver convergence. For this reason,
3794     decide to disable this piece of code.
3795     to recover previous version, just set zeroPsNH = exactConserv (line 78).
3796     Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
3797 jmc 1.1188 o pkg/ggl90:
3798     - fix previous modif (unfortunatly has not been documented here).
3799 mlosch 1.1182 o pkg/seaice/autodiff:
3800 mlosch 1.1185 - add CPP flag to include clipping of zeta in EVP code;
3801     although clipping of zeta is not necessary for EVP and not recommended
3802     it was done by default, now clipping is disabled by default
3803 mlosch 1.1184 - modify computation and store zetaC/Z in seaice_evp for TAF
3804 mlosch 1.1183 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
3805 mlosch 1.1190 - change seaice_calc_viscosities/strainrates for better
3806 mlosch 1.1183 vectorization after AD by TAF
3807 jmc 1.1187 - rearrange common blocks in SEAICE.h once again for easier dumps of
3808 mlosch 1.1182 adjoint output, adjust adcommon.h and g_common.h
3809     - change flux form of default advection scheme for better vectorization
3810     of adjoint code
3811     - modify lab_sea/input.lsr to test the flux form of default advection
3812     scheme
3813 mlosch 1.1181 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
3814     transition in checkpoint61r)
3815    
3816 jmc 1.1203 checkpoint61x (2009/10/19)
3817 heimbach 1.1179 o adjoint: adding two new verification experiments
3818     * tutorial_global_biogeo: an online dic sensitivity experiment
3819     (work with G. Forget)
3820     * tutorial_dic_adjoffline: an offline dic sensitivity experiment
3821     (an update of the Dutkiewicz et al., 2006 paper)
3822     Both use the same CO2FLUX cost function, but different controls
3823     Gradient checks look good, but some recomp. could still be traightened out
3824     Should add xx_dic control variable to test at some point
3825 jmc 1.1178 o model/src:
3826     add run-time parameters to check and/or mask initial Temp & Salt
3827 jmc 1.1177 o pkg/ptracers:
3828     apply zonal filter (if used) to all passive tracers
3829    
3830 jmc 1.1203 checkpoint61w (2009/10/12)
3831 heimbach 1.1175 o adjoint:
3832     * update and finish work on adjoint of dic package (G. Forget)
3833     * start adjoint of offline package
3834     * bug fix for cube-sphere TLM code (active_file_g.F)
3835 jmc 1.1173 o tutorial_global_oce_optim:
3836     now tested with 4 tiles (change data.grdchk and update output_adm.txt)
3837 jmc 1.1174 and add SIZE.h_mpi for MPI testing
3838 mlosch 1.1172 o pkg autodiff
3839     - fix bug in autodiff_restore
3840     - make genmake2 remove comments and empty lines from ad_input_code.f in
3841     order to reduce file size (new script file remove_comments_sed)
3842 jmc 1.1171 o allows to specify vertical profile of vertical viscosity (viscArNr)
3843 mlosch 1.1170 o pkg autodiff
3844     autodiff_ini_model_io: comment out writing of grid information to netcdf
3845     files, because at this time the grid fields are a bunch of zeros
3846     (this is analogous to ini_mnc_vars.F)
3847 mlosch 1.1169 o pkg seaice/autodiff:
3848     left-over from removing the 3-time-level fields:
3849     - small rearrangement of common blocks (SEAICE.h)
3850     - fix field declaration in order to get meaningful output in
3851     adseaice.*.nc (adcommon.h)
3852 jmc 1.1165 o pkg obcs:
3853     - go through NH code only if nonHydrostatic=T
3854     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
3855 jmc 1.1174 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
3856 jmc 1.1166 => Update output of experiment seaice_obcs
3857     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
3858 jmc 1.1167 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
3859 jmc 1.1168 - fix restart for useOBCSprescribe + useEXF
3860 mlosch 1.1164 o pkg ctrl
3861     - make obcs as control parameter work also with useSingleCPUio
3862     - replace a few sny and snx by Ny and Nx to be consistent with
3863     ctrl_set_globfld_x/yz.F
3864 mlosch 1.1163 o pkg seaice
3865     - re-introduce global field frWtrAtm for the case of
3866     ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
3867     - catch the case of an empty filename in seaice_cost_init_fixed.F
3868     o pkg ecco:
3869     - small bug fixes in the_main_loop
3870     . fix order of monitor arguments
3871     . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
3872     . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
3873     that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
3874     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
3875     imbalance diagnostics for wmean_h/sflux = 0
3876     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
3877     - catch the case of empty filenames in ecco_cost_init_fixed.F
3878     and ecco_readparms.F
3879     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
3880 mlosch 1.1164 to make this statement meaningfull in ecco_cost_weights.F
3881 jmc 1.1162 o pkg zonal_filt:
3882     - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
3883     - when using rStar, filter uVel*hFacW instead of uVel
3884     (tested without topography: fix a Pb of growing instability with NLFS)
3885 dfer 1.1161 o pkg/aim/thsice:
3886     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
3887     (works as SST restoring)
3888 dfer 1.1160 o pkg/thsice:
3889     -add specific parameter for salt restoring in slab mixed-layer
3890     (by default equal to the temperature restoring)
3891    
3892 jmc 1.1203 checkpoint61v (2009/09/21)
3893 mlosch 1.1158 o pkg/kpp:
3894     -add double diffusive contributions as a hack, turned off by default
3895     for now, and the code can be excluded with a CPP-flag
3896     EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
3897     -add a verification experiments to "vermix" to test this code
3898 dfer 1.1157 o pkg/mom_common:
3899     Move computation of length scales to mom_init_fixed.F (avoid recomputation
3900     at each time-steps*levels).
3901 rpa 1.1156 o pkg/layers:
3902     Created a new package for computing volume fluxes in temperature or
3903     [not yet implemented] density layers, e.g. for calculating residual
3904     overturning circulations.
3905 jmc 1.1155 o pkg/diagnostics:
3906     implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
3907     o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
3908 jmc 1.1154 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
3909     To avoid mixing type (RS/RL) of input/output array argument,
3910     replace single mixed-type array with a pair from each type (RS/RL).
3911 jmc 1.1153 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
3912     is now implemented for all pkgs (previously only done for the main pickup)
3913    
3914 jmc 1.1203 checkpoint61u (2009/08/25)
3915 mlosch 1.1150 o pkg/obcs:
3916 mlosch 1.1151 - change OB?eta from _RS to _RL and put them into a separate commen block
3917     - add code to read OB?eta from a file via obcs_prescribe_read: the code
3918     compiles and does not destroy any other experiments, the data is read
3919     properly, but the code is not tested in actual applications
3920 mlosch 1.1149 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
3921     create a meaningful unit attribute for the time coordinate variable
3922 jmc 1.1148 o pkg/ebm: add plenty of missing "_d 0" ;
3923     update results of experiment global_ocean_ebm (fwd + adjoint tests)
3924     Notes: several pieces of code only works for (very) specific set up
3925     (domain size, lat range, etc ...); should be documented & stop if one
3926     of those assumptions is not meet.
3927 jmc 1.1147 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
3928     update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
3929     and offline_exf_seaice (seaicetd + adjoint).
3930 jmc 1.1146 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
3931     update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
3932     seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
3933     o few changes to pass when compiling with strick checking of arguments
3934     across S/R (allow to find few bugs in S/R calls).
3935 mlosch 1.1145 o pkg/seaice:
3936     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
3937     2d-fields, for slightly better performance
3938 jmc 1.1146
3939 jmc 1.1203 checkpoint61t (2009/07/22)
3940 mlosch 1.1142 o pkg/seaice:
3941     - remove unused variables in seaice_evp
3942     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
3943 jmc 1.1141 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
3944     named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
3945 jmc 1.1144 each processor opens a different file (a fix from Matt).
3946 jmc 1.1140 o cg2d:
3947     use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
3948     this reduces number of EXCH calls by 2 when using exch2.
3949     For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
3950     directives and missing simple EXCH (exch_s3d_rx) adjoint code.
3951     o pkg/thsice:
3952     add code for Near Infra-Red albedo (from Jeff)
3953 jmc 1.1139 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
3954 jmc 1.1140 o ini_model_io:
3955     move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
3956     MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
3957     to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
3958 jmc 1.1139
3959 jmc 1.1203 checkpoint61s (2009/06/30)
3960 jmc 1.1137 o pkg/exch2 (exch2_rxN_cube*):
3961     remove last BARRIER (no need to synchronise after getting data from shared
3962     buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
3963 jmc 1.1136 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
3964     and generate new output (for the 2 tests) using default rotationPeriod.
3965 jmc 1.1135 o pkg/exch2:
3966     - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
3967     (was already the case with AUTODIFF_EXCH2 defined)
3968     - add bj in exch2 arrays and S/R.
3969 jmc 1.1136 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
3970     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
3971 jahn 1.1134 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
3972     - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
3973     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
3974     - verification experiment natl_box.longstep
3975 jmc 1.1133 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
3976     allow different versions of ifort (8 or 9) and different versions
3977     of mpi (mpich or mpich2) to be used with the same optfile.
3978     requires to load a netcdf module and set MPI_INC_DIR (see comments inside
3979     optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
3980 jmc 1.1135 o pkg/seaice:
3981     fix previous modif (3-level field removed) for old-pickup reading
3982 jmc 1.1133
3983 jmc 1.1203 checkpoint61r (2009/06/25)
3984 mlosch 1.1129 o pkg/seaice:
3985 mlosch 1.1130 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
3986     1. introduce fields for time step (N-1)
3987     2. do not use levels 2 and 3 anymore (but keep them)
3988     3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
3989     includes changes to pkg/thsice/thsice_get_velocity.F,
3990     model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
3991     pkg/obcs/obcs_apply_uvice.F.
3992     - completely remove code for leap-frog time stepping for second order
3993 mlosch 1.1129 advection
3994 heimbach 1.1131 - adjusted adjoint accordingly;
3995     gradient checks have improved by an order of magnitude!
3996 mlosch 1.1130
3997 jmc 1.1203 checkpoint61q (2009/06/22)
3998 mlosch 1.1128 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
3999     - the boundary conditions along open boundaries are unclear, because the
4000     associated masks are set to zero and are thus treated as closed when
4001     applying the slip-boundary conditions.
4002     - move initialisation of grid variables from seaice_init_varia to _fixed
4003 dimitri 1.1127 o adding doc/diags_changes.txt
4004 jmc 1.1126 o model/src:
4005     do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
4006     to avoid "_diags" naming if no relation to pkg/diagnostics.
4007     ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
4008     file and only call PLOT_FIELD_XYZ if debugMode=T.
4009     remove few PLOT_FIELD_XY calls outside initialisation.
4010     remove few unnecessary BARRIER.
4011 dimitri 1.1125 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
4012     of salt_plume package in Southern Ocean
4013 jmc 1.1124 o pkg/thsice:
4014     - fix hOceMxL in overlap (needed for sea-ice advection);
4015     update output of experiment global_ocean.cs32x15.icedyn.
4016 mlosch 1.1123 o pkg/seaice:
4017     - make the (placeholder-)tracer IceAge a little more meaningful
4018 mlosch 1.1122 by avoiding ridging of age due to convergent ice flow
4019 dimitri 1.1127 - add diagnostics for surface temperature, atmospheric and oceanic
4020     heat flux, and atmospheric and oceanic ice growth
4021 mlosch 1.1122
4022 jmc 1.1203 checkpoint61p (2009/06/10)
4023 jmc 1.1120 o eesupp (global_max & global_sum):
4024     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
4025     - remove starting & endding barrier (no longer needed)
4026 jmc 1.1119 o pkg/mdsio, writelocal:
4027     works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
4028     (remove the STOP): uses shared buffer IO to store data from all threads
4029     and then let master-thread write nThreads tiles.
4030 jmc 1.1118 o pkg/mdsio (read/write field):
4031     - tiled IO done in 1 piece (all levels at a time);
4032 jmc 1.1119 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
4033 jmc 1.1118 - multi-threaded: allow to read/write local (non-shared) array
4034     (was already working with singleCpuIO ; now works also without);
4035     => no longer needs barrier call after reading a file (added inside
4036 jmc 1.1119 mds_read/write field).
4037 jmc 1.1118 - move barrier calls outside gather/scatter_2d to mds_read/write_field
4038 mlosch 1.1115 o pkg/obcs/exf
4039 mlosch 1.1116 - exf_getffieldrec.F: add a few ". _d 0" and
4040     add code to catch the case fldperiod = 0.
4041 mlosch 1.1115 - obcs_precribe_read.F: change if statements so that they match
4042     the variable type (_RL)
4043     - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
4044     exf_iprec) as part of namelist EXF_NML_01
4045 jmc 1.1114 o pkg/mdsio:
4046     - read/write tiled (local) files: read/write 1-level tile chunk at a time
4047     (instead of segment of length sNx); expected to speed up tiled IO.
4048     o pkg/exch2:
4049 jmc 1.1113 - take buffer copy from/to array out of S/R exch2_send/recv into new
4050     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
4051     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
4052     - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
4053 jmc 1.1114 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
4054 jmc 1.1113 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
4055     including Topology header file (and common blocks).
4056     - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
4057     remove 2nd exch call in exch2_s3d_rx (no longer needed).
4058     - document S/R arg. list (+ update some comments)
4059 dimitri 1.1117 o pkg/seaice:
4060     - added SEAICE_CLIM_AIR code, which permits modulation of surface air
4061     temperature and humidity over sea ice based on climatological values.
4062 mlosch 1.1111 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
4063     of LSR (this change is expected to change the results slightly because now
4064     it uses slightly difference moduli from the second last LSR solution, but
4065     that is more consistent with the stress computations; this part of the code
4066     is not tested in the verification experiments)
4067 mlosch 1.1110 - fix diagnostics for flux of ice in case of B-grid
4068     - turn strain rates eij and press into global fields within global
4069     common block in SEAICE.h for more straighforward diagnostics
4070     - fix diagnostics for principal stress components, press, zeta, eta
4071     to give something meaning full
4072 jmc 1.1109 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
4073     new output (all 4 tests) using default rotationPeriod.
4074 dfer 1.1112 o pkg KPP:
4075     - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
4076     - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
4077     and normal grid from 1 to Nr)
4078 dfer 1.1108 o Fix computations of L4rdt in mom_calc_visc.F
4079 jmc 1.1107 o eesupp:
4080     new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
4081     should be called before a "stop" if we know that all process are going
4082     to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
4083    
4084 jmc 1.1203 checkpoint61o (2009/05/26)
4085 jmc 1.1106 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
4086     o model/src/ini_curvilinear_grid.F:
4087 mlosch 1.1104 compute angleSin/CosC when they are not read from a file
4088 jmc 1.1106 o pkg/seaice:
4089 mlosch 1.1104 add pseudo time stepping for LSOR
4090 jmc 1.1103 o pkg/exch2:
4091     temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
4092 dimitri 1.1102 o pkg/seaice:
4093 dimitri 1.1105 Adding separate sea ice albedo, drag coefficients, and HO in Southern
4094     Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
4095 jmc 1.1101 o SingleCpuIO:
4096     fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
4097     o pkg/seaice:
4098 jmc 1.1100 put exchanged variable in (local) common block for MPI+Multi-Threads
4099     to work (necessary with exch1, and for now with exch2 too).
4100 jmc 1.1099 o verification: to get more experiments tested with mpi, mth and mpi+mth,
4101     change tiling of:
4102     aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
4103     hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
4104     update output of exp:
4105     exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
4106     tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
4107     + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
4108     (note: output.txt generated on faulks using only 1 tile)
4109 jmc 1.1098 o eesupp & mdsio (SingleCpuIO):
4110     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
4111     parameter "W2_useE2ioLayOut" (read from file "data.exch2").
4112     Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
4113     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
4114     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
4115     gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
4116 jmc 1.1097 o pkg/exch2:
4117     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
4118     read parameter file "data.exch2" if it exists; otherwise try default regular
4119     cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
4120     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
4121     with new code (not to be used, just as a backup solution).
4122 jmc 1.1098 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
4123     in utils/exch2/input.
4124 jmc 1.1097
4125 jmc 1.1203 checkpoint61n (2009/05/12)
4126 jmc 1.1095 o eesupp & mdsio (SingleCpuIO):
4127     - move mapping to global io-buffer inside gather_2d/scater_2d: this save
4128     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
4129     receive real*4 array (instead of real*8) to read/write 32.bit files.
4130     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
4131     and remove new mapping S/R)
4132 jmc 1.1094 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
4133     - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
4134     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
4135     when using exch2. Add S/R to map global io-buffer to global model array.
4136     - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
4137    
4138 jmc 1.1203 checkpoint61m (2009/04/29)
4139 jmc 1.1094 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
4140     and add 3 other S/R for other types (R4,R8,RS).
4141 jmc 1.1092 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
4142     o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
4143     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
4144     - reduce number of macro definitions (keep only those which are used);
4145     can always call directly the corrresponding S/R if needed.
4146 jmc 1.1094 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
4147 jmc 1.1092 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
4148     Fixed wrong type of arg in:
4149 jmc 1.1094 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
4150 jmc 1.1092 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
4151     To fix: global_sum of var in common block is wrong (multi-threaded) in:
4152     dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
4153     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
4154 jmc 1.1094 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
4155     "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
4156 jmc 1.1091 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
4157     o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
4158     edges are closed (zero depth); might happen with "blank tiles";
4159 jmc 1.1094 for now, disabled if using OBCS.
4160 jmc 1.1091 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
4161 jmc 1.1090 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
4162 jmc 1.1091 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
4163 jmc 1.1089 to reduce length of 1.D array print in STDOUT.
4164 jmc 1.1088 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
4165     + use 48 tiles (16x8): this will allow to test "blank tiles".
4166     o start to test MPI + multi-threaded (change testreport to skip tests
4167     where number of tiles do not match).
4168     o genmake2: add option "-omp" to turn on Open-MP ;
4169     passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
4170 jmc 1.1086 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
4171     and keep the original tile numbering. Note: compatible with old
4172     W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
4173    
4174 jmc 1.1203 checkpoint61l (2009/04/07)
4175 jmc 1.1085 o Overlaps had been forgotten in calculating ijk keys : fixed
4176     o fix cyrus makedepend for gcc 4.4
4177 jmc 1.1084 o experiment fizhi-cs-aqualev20:
4178     switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
4179 jmc 1.1088 and generate new output. Note: new output is much closer to the old
4180     one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
4181 jmc 1.1084 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
4182     o pkg/fizhi:
4183     - change to avoid indices going deliberately over array-bounds
4184     - remove unnecessary MPI stuff
4185     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
4186     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
4187     does not go over array-bounds and therefore returns reliable output.
4188     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
4189     this S/R has 4 output arguments, which are used inside "get_alarm";
4190     when it is called with the same variable "ndum" in place of several
4191     output arguments, this produces weird side effect inside "get_alarm"
4192     (e.g., datein=dates(n) is overwritten by timein=times(n) since both
4193     datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
4194     address) and produces error.
4195 jmc 1.1090 o tools/gemake2: (March 27-29 2009)
4196     with option "-mpi": link *_mpi files from "MODS" dir (this is what
4197     testreport does).
4198 jmc 1.1083 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
4199 jmc 1.1084 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
4200 jmc 1.1083 update lab_sea.lsr & lab_sea.salt_plume results
4201 mlosch 1.1079 o pkg/seaice:
4202     Major overhaul of the LSOR solver: change discretization from original
4203     finite differences to finite volume. The old routine is still in the
4204     file seaice_lsr.F and can be turned on with the CPP-flag
4205     SEAICE_OLD_AND_BAD_DISCRETIZATION
4206     Along with this change, the discretization of the strain rates is changed.
4207     The same flag turns on the old discretization in seaice_calc_strainrates.F
4208     All verification experiments with seaice are affected (except for
4209     seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
4210     results by setting the above flag.
4211     Further changes involve changes in defaults:
4212     - ALLOW_FLOODING is defined and turned on by default
4213 heimbach 1.1087 - SEAICEadvSnow = .true. is now the default
4214     - SEAICEadvSalt = .true. is now the default
4215     - SEAICEadvAge = .true. is now the default
4216 mlosch 1.1081 - SEAICE_clipVelocities = .false. is now the default
4217     (as per J. Zhang's recommendation)
4218 mlosch 1.1079 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
4219     is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
4220     - seaice_growth: replace computation of UG by a simple copy from wspeed
4221    
4222 jmc 1.1203 checkpoint61k (2009/03/18)
4223 mlosch 1.1078 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
4224     seaice_lsr: fixed a few metric terms,
4225     affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
4226     add more debugging diagnostics
4227     seaice_evp: removed superfluous many metric terms of FV discretization
4228     of stress divergence
4229     affects lab_sea, lab_sea.hb87
4230     seaice_ocean_stress: removed superfluous many metric terms of FV discretization
4231     of stress divergence for non-evp solver
4232     (this part is not tested anywhere)
4233     seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
4234     they were effectively only half slip
4235     affects lab_sea.hb87
4236 jmc 1.1082 updated all relevant verification experiments (except lab_sea//output_adm.txt
4237     which was left over, but fails at level 7 & 6)
4238 mlosch 1.1078
4239 jmc 1.1203 checkpoint61j (2009/03/17)
4240 mlosch 1.1076 o pkg/seaice: turn a few hard wired parameters into run time parameters
4241 mlosch 1.1075 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
4242     time in seconds as promised by the usints in seaice_monitor and exf_monitor
4243 mlosch 1.1074 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
4244     that are not cubed-sphere grids
4245 mlosch 1.1073 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
4246 jmc 1.1072 o pkg/ctrl:
4247     fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
4248 jmc 1.1071 o non-hydrostatic (calc_gw.F):
4249     fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
4250     update output of exp. global_ocean.cs32x15.viscA4
4251     o remove backward compatibility for thetaMin,phiMin
4252 jmc 1.1070 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
4253 mlosch 1.1069 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
4254     interpolated wind field not only for curvilineargrid=.true., but also
4255     for a rotated grid (rotateGrid=.true.)
4256 mlosch 1.1068 o pkg/exf: add capability to bypass interpolation for runoff
4257     by setting yet another CPP-flag
4258 jmc 1.1070 o eesupp/src, B-grid exchange:
4259     add simple (6 tiles, non MPI) CS exch + standard interface S/R.
4260 heimbach 1.1067 o autodiff
4261     new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
4262     allows to switch to single-prec common blocks;
4263     corresponding switch occurs in tamc.h, integer isbyte
4264     TAF store directivs "byte" and "kind" seem equivalent;
4265     Most tamc.h have been updated correspondingly.
4266    
4267 jmc 1.1203 checkpoint61i (2009/02/13)
4268 heimbach 1.1066 o autodiff:
4269     fix autodiff_sore/_restore indices for obcs
4270     (spotted by I. Hoteit, M. Mazloff)
4271 heimbach 1.1065 o pkg/autodiff, pkg/ctrl:
4272     Add flag to reduce all tapelev I/O to single-prec.
4273     In data.ctrl set
4274     doSinglePrecTapelev = .TRUE.
4275 jmc 1.1070 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
4276     check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
4277 mlosch 1.1062 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
4278     real fresh water flux (not yet)
4279 jmc 1.1060 o pkg/mdsio & rw:
4280     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
4281     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
4282 jmc 1.1058 o pkg/flt:
4283     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
4284     init_fixed & ini_varia.
4285 jmc 1.1059 - clean-up & simplify linear interpolation S/R:
4286     move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
4287     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
4288 jmc 1.1060 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
4289 jmc 1.1061 - add vert. coordinate & horiz. indices to output files.
4290     - change vertical position in initial condition, from index to depth [m].
4291 jmc 1.1063 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
4292     (easier to get to a curvilinear grid) ; delX,delY no longer used.
4293 dfer 1.1057 o pkg/ggl90: a few modifications:
4294     - fix bottom boundary condition, and interpolation of KappaE
4295     near top and bottom
4296     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
4297     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
4298     - add a few options for mixing-length upper limit (--> mxlMaxFlag)
4299 jmc 1.1056 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
4300     (maintain temporary backward compatibility, until next checkpoint)
4301    
4302 jmc 1.1203 checkpoint61h (2009/01/27)
4303 jmc 1.1054 o pkg/diagnostics with "periodic averaging diagnostics":
4304     fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
4305 jmc 1.1053 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
4306 mlosch 1.1052 o pkg/obcs: fix loop ranges for balancing code
4307 jmc 1.1051 o pkg/flt:
4308     - improve criteria for finding which tile owns a float.
4309     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
4310 dfer 1.1050 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
4311     aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
4312     with ocean biogeo)
4313 jmc 1.1049 o pkg/flt:
4314     - do some cleaning and fix the restart ;
4315     - add output.txt in flt_example/results to get this pkg tested.
4316     o genmake2: add an EXTENDED_SRC option and flag.
4317     for now, cannot be turned on on command line (only through genmake_local)
4318 jmc 1.1048 o pkg/mdsio: read/write vector:
4319     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
4320 jmc 1.1049 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
4321 jmc 1.1048 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
4322     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
4323     (drop to 4 digits matching for grad). But this test does not look very
4324     reliable (was already failling on eddy, fc5, at 6.digits). Update output.
4325    
4326 jmc 1.1203 checkpoint61g (2008/12/29)
4327 jmc 1.1046 o pkg/flt:
4328     - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
4329     + make OPTIONS file more standard.
4330     - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
4331     - fix _BYTESWAPIO CPP-Flag
4332     - standard reading of file-parameter "data.flt"
4333 jmc 1.1047 - fix argument list of S/R FLT_RESTART
4334 jmc 1.1046 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
4335 mlosch 1.1045 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
4336 mlosch 1.1044 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
4337     a still unfixed compiler/optimization bug
4338    
4339 jmc 1.1203 checkpoint61f (2008/11/21)
4340 jmc 1.1042 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
4341     update results of global_ocean.cs32x15.icedyn test.
4342 jmc 1.1041 o move getcon.F from model/src to pkg/fizhi.
4343 jmc 1.1040 o pkg/exf: add parameter for extrapolation of temp up to the surface
4344     and option to prevent negative evap (in bulk_largeyeager04 only).
4345 jmc 1.1039 o Prather Advection scheme: fix tracer conservation for divergent flow
4346     (e.g., when using NonLin Free-Surface).
4347 dfer 1.1038 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
4348 jmc 1.1037 o gmredi (Visbeck-variable-K):
4349     - add more parameters to Visbeck-variable-K.
4350     - use a 5 points average for dSigmaR in Visbeck-K calculation
4351     (more "homogenous": same stencil and same weights as in dSigmaH)
4352     - update output of ideal_2D_oce experiment.
4353 mlosch 1.1034 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
4354     (#undef REAL4_IS_SLOW)
4355     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
4356     coordinate variable
4357     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
4358     (surface forcing fields), removes some of the functionality
4359     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
4360     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
4361     probably not all: copy _RS surface flux fields to RL field before
4362     calling DIAGNOSTICS_FILL
4363 mlosch 1.1035 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
4364     real*4 (CALL EXCH_*_RS) versions.
4365 jmc 1.1036 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
4366     (generate new output).
4367 mlosch 1.1034
4368 jmc 1.1203 checkpoint61e (2008/10/23)
4369 jmc 1.1032 o gmredi (Visbeck-variable-K):
4370     - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
4371     - change computation of Visbeck-K where Slope > Smax :
4372     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
4373     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
4374 jmc 1.1031 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
4375     to be the same as with Z-coord. (i.e., m/s & no-units respectively).
4376     o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
4377 jmc 1.1030 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
4378 jmc 1.1032 does not become too large (to avoid precision problems in implicit-diffusion
4379 jmc 1.1030 solver); update ideal_2D_oce output.
4380 dfer 1.1028 o pkg ggl90:
4381     - in ggl90_cal.F: compute only one set of visc/diff, used to
4382     step forward TKE/T/S/momentum
4383     - default value of GGL90viscMax/GGL90diffMax larger and equal (to
4384     have Prandlt =1)
4385 jmc 1.1032 o gmredi (fm07):
4386 jmc 1.1029 - add lower limit on Transition layer thickness + lower limit on 1/lambda
4387 jmc 1.1027 - allow to set few more params from data.gmredi
4388 dfer 1.1026 o pkg ggl90:
4389     - add missing sqrt(2) factor in computation of mixing length
4390     scale in ggl90_calc.F
4391     (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
4392    
4393 jmc 1.1203 checkpoint61d (2008/09/25)
4394 heimbach 1.1025 o adjoint modifs
4395     - adapt to new field rhoInSitu
4396     - allow to revert from StoreDynVars2D, StoreDynVars3D
4397     to individual fields
4398     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
4399 jmc 1.1024 o store 3-D (in-situ) density in commom block (DYNVARS.h)
4400     - save 1 rho computation.
4401     - no longer modify T & S inland when using down_slope pkg.
4402 jmc 1.1023 o gad_som : allow to switch to SOM advection for T & S without corresponding
4403     pickup files (using new S/R: MDS_CHECK4FILE).
4404     o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
4405     (for useSingleCpuIO to work in multi-threaded)
4406 mlosch 1.1022 o pkg/shelfice:
4407     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
4408     with SHELFICEtopoFile in data.shelfice
4409     - move code for reading ice shelf topography and modifying hFacC into separate
4410     subroutines of the shelfice package
4411     - separate initialisation of "fixed" and "variable" variables
4412     - kTopC is not (yet) replaced by kSurfC, although this is possible
4413 jmc 1.1023 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
4414 jmc 1.1020 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
4415     and rename:
4416     ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
4417     ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
4418     o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
4419    
4420 jmc 1.1203 checkpoint61c (2008/08/30)
4421 jmc 1.1018 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
4422     to add mass source/sink of fluid in the interior (3-D generalisation
4423     of oceanic real-fresh water flux).
4424     o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
4425 jmc 1.1017 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
4426 jmc 1.1016 o new pkg: down_slope
4427     density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
4428     - presently, modify T & S inland (dwnslp_calc_rho.F).
4429     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
4430     - implementation for ocean in P-coords not tested.
4431     - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
4432     o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
4433 jmc 1.1015 (to facilitate conversion of oceanic pkg to p-coordinate).
4434 jmc 1.1014 o change FIND_RHO to FIND_RHO_2D :
4435     pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
4436     o new pkg: cheapaml
4437    
4438 jmc 1.1203 checkpoint61b (2008/08/05)
4439 jmc 1.1011 o exch2:
4440 jmc 1.1012 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
4441     - no longer depend on the order sequence (N,S,E,W).
4442     - 3rd exchange no longer needed (tested with 24 tiles).
4443     - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
4444     - exch_UV_A-grid readily available (but not yet tested).
4445     comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
4446     (both are no longer needed) in exch_uv: no effect in forward run; but
4447     get truncation error differences with adjoint exch.
4448     o exch2:
4449 jmc 1.1011 - change index-bounds storage (moved from target to local tile,
4450     more intuitive this way) ; rename/remove some variables.
4451 jmc 1.1012 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
4452 jmc 1.1011
4453 jmc 1.1203 checkpoint61a (2008/07/29)
4454 jmc 1.1009 o exch2/matlab-topology-generator:
4455     fix bug in index bounds for N-S internal exchange (hard to tell if this
4456     had any effect on the solution).
4457 mlosch 1.1008 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
4458     is exceeded
4459 mlosch 1.1007 o testreport: modify syntax of awk, so that it works also with
4460     awk, and not only with nawk and gawk
4461    
4462 jmc 1.1203 checkpoint61 (2008/06/24)
4463 heimbach 1.1005 o autodiff
4464     Change default for TAF usage by removing argument '-nonew_arg'
4465     This changes TAF subroutine argument list (ordering of active var.)
4466     Omission of this flag leads to incompatibility w.r.t. TAMC
4467     To restore TAMC-compatibility, need following modifs:
4468     * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
4469     * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
4470     Tested TAF version is 1.9.22
4471     N.B.: exch2 hand-written adjoint code currently not TAMC compatible
4472    
4473 jmc 1.1203 checkpoint60 (2008/06/19)
4474 heimbach 1.1004 --->>> This is the last checkpoint for which generating the adjoint
4475     --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
4476     --->>> by default.
4477     --->>> Future checkpoints will ommit this flag by default.
4478 jmc 1.1003 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
4479 gforget 1.1002 o pkg/grdchk: Add gradient check to etan0 perturbations.
4480 gforget 1.1001 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
4481 gforget 1.1000 o pkg/autodiff: more flexibility in zeroadj.
4482     model/src: modifying do_oceanic_phys.F accordingly.
4483 gforget 1.999 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
4484     o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
4485     special setup of gmredi for which the adjoint is stable
4486     enough for parameter optimization.
4487 gforget 1.998 o bridging the gap between eddy stress and GM.
4488     -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
4489     along with a change in CPP option (now ALLOW_EDDYPSI).
4490     -> when using GM w/ GM_AdvForm:
4491     The total eddy streamfunction (Psi = eddyPsi + K x Slope)
4492     is applied either in the tracer Eq. or in momentum Eq.
4493     depending on data.gmredi (intro. GM_InMomAsStress).
4494     -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
4495     The key modifications are in model/src/taueddy_external_forcing.F
4496     pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
4497 jmc 1.1003
4498 jmc 1.1203 checkpoint59r (2008/05/29)
4499 jmc 1.996 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
4500     from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
4501     fix option to read coriolis(@ cell-corner) from files with CS-grid.
4502 mlosch 1.995 o pkg/mnc: add some attributes to standard 1D-coordinate variables
4503 mlosch 1.993 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
4504     mass points, when using mnc for output
4505     - add runtime parameter (missing_value, missing_value_int) to override
4506     default (which is the value of getcon('UNDEF'))
4507     o pkg/mnc: prepare mnc for the actual use of missing values with the
4508     diagnostics package: small fix in mnc_cw_readwrite.template and more
4509     initialisation of never used fields
4510 mlosch 1.994 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
4511     versions
4512     o pkg/thsice/thsice_ini_vars.F added default initial values so that
4513     thermodynamics sea ice solver does not blow up when some initial fields
4514     are missing.
4515 jmc 1.991 o move from external_forcing_surf.F to ini_forcing.F
4516     the p-coord. hack consisting in using pLoad to set phi0surf ;
4517     update output of tutorial_global_oce_in_p (affected @ truncation level).
4518 dfer 1.990 o Freshen up a bit hs94.1x64x5, notably:
4519 mlosch 1.994 remove rotationPeriod and tRef=5*0. (adjoint only), and add
4520     exactConserv=.TRUE.
4521 jmc 1.989 o pkg/generic_advdiff:
4522     change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
4523     applies to files where Temperature & Salinity 2nd Order moments are used.
4524 jahn 1.988 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
4525     this uses a dynamically allocated internal state data structure
4526     (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
4527     and requires a fortran 90 compiler
4528    
4529 jmc 1.1203 checkpoint59q (2008/05/06)
4530 jmc 1.986 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
4531     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
4532 dfer 1.985 o Refresh tutorial_global_oce_biogeo, notably:
4533     - change bathymetry (put back seamounts in ACC, use hFacs)
4534     - change EOS (POLY3 --> JMD95Z)
4535     - use Bryan-Lewis vertical diffusivity
4536     - use multidimensional advection
4537     - remove old virtual virtual in dic pkg, now done through ptracer pkg
4538     - change a couple of parameters in dic pkg
4539 gforget 1.984 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
4540 mlosch 1.982 o pkg/obcs: change default to OBCSfixTopo = .true.,
4541 mlosch 1.983 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
4542     - replace "debugMode" with "debugLevel .GE. debLevB"
4543 gforget 1.981 o implementation of TAF directives for gchem,cfc,dic
4544 jmc 1.980 o remove "exp5" (replaced by tutorial_deep_convection).
4545 mlosch 1.979 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
4546     this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
4547     the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
4548 mlosch 1.982 --> changes results in exp4, seaice_obcs
4549 jmc 1.980 o tutorial_deep_convection :
4550 jmc 1.978 update the set-up and increase resolution and domain size ; start
4551     from pseudo initial conditions = output at t=120mn in order to see
4552     something happening when running testreport.
4553 mlosch 1.976 o pkg/seaice: add os7mp as an advection scheme
4554     add check for advection schemes
4555 mlosch 1.977 add a flag for restoring T and S underneath sea ice
4556 mlosch 1.975 o pkg/my82: add netcdf-support and diagnostics
4557 dfer 1.974 o thsice pkg:
4558 mlosch 1.979 - Now hsMax limits snow height by turning it into ice following
4559 dfer 1.974 flooding scheme (and now conserving energy)
4560     - Slight rewriting of the formula in thsice_calc_thick.F
4561     - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
4562 jmc 1.980 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
4563 dfer 1.974
4564 jmc 1.1203 checkpoint59p (2008/04/10)
4565 jmc 1.973 o gchem / dic / cfc :
4566     - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
4567     - add new parameter files: "data.dic" & "data.cfc" ;
4568     - various re-arrangement in initialisation & header file ;
4569     - fix tutorial_global_oce_biogeo for multi-threaded test.
4570     o pkg/dic: test for "pickup_dic" file when restarting ;
4571     if no pickup-file, can restart with a re-initialised pH (same as it did
4572 jmc 1.972 before) providing pickupStrictlyMatch is set to False.
4573 jmc 1.971 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
4574     + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
4575 jmc 1.970 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
4576     and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
4577     o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
4578     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
4579     (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
4580 jmc 1.969 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
4581     scheme to use for vorticty-term ;
4582     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
4583     (with default selectVortScheme, return to original discretisation)
4584     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
4585 mlosch 1.968 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
4586 jmc 1.967 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
4587     bottom ; only used with variable horizontal viscosity and non-hydrostatic.
4588     also fix diagnostics VISCAHW & VISCA4W.
4589    
4590 jmc 1.1203 checkpoint59o (2008/03/07)
4591 jmc 1.965 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
4592 mlosch 1.964 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
4593     move a few statemens out the main loop into separate loops
4594 mlosch 1.962 o pkg/shelfice:
4595     - sort out freshwater flux; convert freshwater fluxes to mass fluxes
4596     (kg/m^2/s), does not break tests, because in verification/isomip,
4597     rhoConstFresh=rhoConst (by accident)
4598 mlosch 1.963 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
4599     - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
4600     new file model/src/seawater.F, so that they are available for all pkgs.
4601     - convert potential temperature into in-situ temperature. This changes the
4602     isomip tests => update tests
4603 mlosch 1.961 o add a flag writePickupAtEnd (default=true) to be able to suppress
4604     writing a pickup at the last timestep
4605 jmc 1.966 o tools/mpack-1.6 :
4606     - disable automake (not working) and autoconf (not needed).
4607     - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
4608     also cleaner with much less compilation warnings.
4609 gforget 1.960 o pkg/profiles:
4610     rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
4611     (for "less than 32 characters name" compiler requirement)
4612 dimitri 1.959 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
4613     conditions that have a different sampling frequency than S/T/U/V obcs
4614 jmc 1.958 o pkg/diagnostics (stats-diags):
4615     - fix global Min/Max in case 1 processor get only empty tiles
4616 mlosch 1.957 o genmake2: replace (4 times)
4617     make genmake_tc_1.o >> genmake_warnings 2>&1
4618     with
4619     COMM="$CC $CFLAGS -c genmake_tc_1.c"
4620     echo $COMM >> genmake_warnings
4621     $COMM >> genmake_warnings 2>&1
4622     to make genmake2 always see the value of CC as specified in the optfile.
4623 jmc 1.956 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
4624     - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
4625     - modify verification advect_cs test to test SOM-advection on CS-grid.
4626 gforget 1.955 o pkg/ctrl:
4627     - Rewrite of ctrl_map_ini_ecco.F,
4628     introducing a generic routine (ctrl_map_ini_gen.F).
4629     - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
4630 jmc 1.956
4631 jmc 1.1203 checkpoint59n (2008/02/09)
4632 jmc 1.953 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
4633     number in dedicate array "hdiag":
4634     - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
4635     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
4636     - many small changes (integer format) for large number of diagnostics
4637     - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
4638     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
4639 mlosch 1.952 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
4640     usingSphericalGrid, this allows to define the rotated grid coordinates
4641     via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
4642     geographical coordinates according to the inverse of the rotation defined
4643     by the Euler angles, so that Coriolis parameter and online-interpolation by
4644     exf works with the geographical coordinates on XC/YC/XG/YG.
4645     Naturally, this feature does not work with all packages, so some
4646     combinations are prohibited in config_summary (flt, flt_zonal, ecco,
4647     profiles), because there the coordinates are assumed to be regular
4648     spherical grid coordinates.
4649 gforget 1.951 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
4650     - introduce isopycnal diffusion coefficient control.
4651     o tools/adjoint_options:
4652     - additional control vector components.
4653 mlosch 1.950 o pkg/mnc: have mnc create marginally meaning full coordinate variables
4654     (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
4655 jmc 1.948 o pkg/mypackage:
4656     - add example of read/write pickup for state-var ;
4657     - add entry points to the main code for state-vars diags & write-pickup.
4658 dimitri 1.946 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
4659     transitions for useExfYearlyFields
4660 mlosch 1.947 - add new subroutine that determines the file to read from for
4661     use*YearlyFields = .TRUE. and .FALSE.
4662 mlosch 1.949 - add a verification experiment to global_with_exf that tests
4663     useExfYearlyFields with USE_EXF_INTERPOLATION defined
4664 mlosch 1.945 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
4665     analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
4666     subroutines (which could be generated from a template, because they are
4667     almost identical), for now they are included in obcs_prescribe_read.F for
4668     simplicity
4669 mlosch 1.943 o pkg/exf:
4670     - add a little more diagnostic to exf_interp_read (in analogy to
4671     mds_read_field, can be turned off with debugLevel < debugLevA=1)
4672     - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
4673 mlosch 1.944 ugly but fast by unrolling short inner loops, inserting a unroll=8
4674     directive in routine lagran, and splitting a loop and making do while the
4675     outermost loop (the latter requires the intoduction of index arrays)
4676 dimitri 1.942 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
4677 dimitri 1.941 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
4678     http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
4679 dimitri 1.940 o verification/seaice_obcs: updated for restart test and latest options
4680 mlosch 1.939 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
4681     ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
4682     for now this is only available for the C-grid code and also within
4683     #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
4684    
4685 jmc 1.1203 checkpoint59m (2008/01/14)
4686 dimitri 1.936 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
4687     and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
4688 dimitri 1.937 o gad_som : fix flux output (& diagnostics) to have same units as other
4689     advection scheme fluxes (was previously multiplied by deltaT).
4690 dimitri 1.933 o added verification/seaice_obcs both to test seaice open boundaries
4691     and to provide an example matlab scrpt for generating them
4692     o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
4693 atn 1.931 o pkg/salt_plume: clean up salt_plume_frac.F to
4694     remove redundancy in PlumeMethod 1 and 4
4695 atn 1.930 o pkg/kpp: added saltplume diagnostics
4696 dimitri 1.929 o pkg/obcs and pkg/seaice:
4697     - do not set uice and vice to zero when OB*icefile are unspecified
4698     - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
4699     - moved seaice tracer obcs after call to seaice_growth
4700 dimitri 1.927 o pkg/salt_plume: added various options for salt plume depth
4701     criterion and for vertical distribution of the salt
4702 jmc 1.928
4703 jmc 1.1203 checkpoint59l (2007/12/18)
4704 jmc 1.925 o pkg/ptracers: new version of ptracers pickup:
4705     read meta file and write only fields which are needed to restart.
4706     ( same logic as main pickup file ; also using pickupStrictlyMatch )
4707 dimitri 1.924 o pkg/seaice:
4708 mlosch 1.923 - add timescale for melting due to warm mixed layer as a means of
4709     setting SEAICE_availHeatFrac more conveniently
4710     - add a CPP-flag/runtime parameter check for flooding algorithm
4711 dimitri 1.924 - reformulated availHeat in seaice_growth.F to be independent of AREA
4712 mlosch 1.923 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
4713     unit changes
4714 dimitri 1.921 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
4715 mlosch 1.919 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
4716     SX vector computer.
4717 dimitri 1.920 o pkg/seaice:
4718     - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
4719     seaice forcing fields can now be read only through pkg/exf
4720     - removed some unused halos
4721 jmc 1.917 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
4722 dimitri 1.922 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
4723     or U/VICE from U/VWIND before computing U/VSTRESS
4724 dimitri 1.916
4725 jmc 1.1203 checkpoint59k (2007/11/30)
4726 dimitri 1.914 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
4727     dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
4728 jmc 1.913 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
4729 jmc 1.925 all experiments pass when compile with un-initialised var. checking option.
4730 dimitri 1.912 o added pkg/salt_plume
4731 jmc 1.911 o script to test restart (for now, in MITgcm_contrib/jmc_script)
4732     o pkg/seaice: new read/write pickup version.
4733     read meta file and write only fields which are needed to restart.
4734     ( same logic as main pickup file ; also using pickupStrictlyMatch )
4735 mlosch 1.910 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
4736 jmc 1.909 o lab_sea.hb87: modify the domain & update output.hb87.txt :
4737     lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
4738     at j=1 & j=Ny+1 : this case is not treated correctly in the restart
4739     process. Fixed here by closing the domain at the Northern boundary.
4740     o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
4741     o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
4742     a set of consecutive levels in/from a 3-D array.
4743 jmc 1.908 o pkg/ptracers:
4744 jmc 1.909 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
4745 jmc 1.908 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
4746    
4747 jmc 1.1203 checkpoint59j (2007/11/09)
4748 jmc 1.906 o in pkgs: dic, obcs, offline, rbcs:
4749     standard way to compute coeff. for time interpolation between 2 time reccords
4750     which retains full precision (& make results less dependent on compiler).
4751     update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
4752 mlosch 1.905 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
4753     packages instead of reading ice cover and wind speed separately
4754 jmc 1.904 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
4755     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
4756     to allow to compile customized code before the update)
4757 jmc 1.903 o cleaning-up:
4758     - fix CPP instruction syntax in pkg/obcs
4759     - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
4760     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
4761     - fix some threads issue in IO parts.
4762 dfer 1.901 o pkg/dic:
4763     - add tons of "_d 0" (--> much better testreports !)
4764     and then update outputs of tutorial_global_oce_biogeo
4765 jmc 1.900 o pkg/mom_fluxform:
4766     add a special version of momentum advection intended to conserve momentum
4767     next to a bathymetry step or a coastline edge. (default = off = #undef)
4768 jmc 1.898 o new read/write pickup version:
4769     - for now, only implemented for main (mdsio) pickup file.
4770     - write out only what is needed to restart; merge pickup_nh , pickup_ph
4771     and main pickup together.
4772     - read meta file; read only what is needed to restart; stop if a field
4773     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
4774     if it make sense (even if the restart is not perfect).
4775     - if no meta file, assume that pickup to read corresponds exactly to
4776     a pickup that would currently be written.
4777     - read pickup written in the old format (until checkpoint59i) if it
4778     recognizes an old meta file (no field-list).
4779     - add a meta file in exp. which starts from a pickup: 2 cases:
4780     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
4781     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
4782     b) a meta file describing the content of the associated pickup file
4783     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
4784     o pkg/mdsio & pkg/rw:
4785     - new routine to read a meta file ; new set of routine to read
4786     Multiple-fields file (with meta file).
4787 dimitri 1.899 o added open boundary conditions capability for seaice
4788     HSNOW, HSALT, UICE, and VICE
4789 dimitri 1.897
4790 jmc 1.1203 checkpoint59i (2007/10/21)
4791 heimbach 1.895 o adjoint:
4792     * fix multiDimAdvection adjoint
4793     (partial recomputation problem by TAF for fVerT(:,:,kDown)
4794     and comlev1 size definition (maxpass vs. max. number of tracers)
4795     * verification/global_ocean.90x45x15 adjoint now tests
4796     NLFS and multiDimAdvection using DST3 (=30)
4797     * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
4798 jmc 1.894 o pkg/kpp: add "_d 0" to real constant (if missing);
4799     update output of exp: natl_box (10.digits); vermix (std, 7.digits)
4800     and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
4801 jmc 1.893 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
4802     for internal parameters related to restart process (formerly from PARAMS.h)
4803     and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
4804     o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
4805     as argument. (only atm2d & obcs write_pickup have not yet been updated)
4806 jmc 1.892 o pkg/monitor:
4807     - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
4808     - fix mon_stats_rs (statistics over the full domain, even where field is zero)
4809     - account for deep Atmosphere factor and density factor (anelastic)
4810 dimitri 1.891 o added open boundary conditions capability for seaice HEFF and AREA
4811 mlosch 1.890 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
4812     thermodynamics
4813     - requires a little reorganization, which affects the testreport results
4814     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
4815     so that now the conservative form is tested
4816     - add a few comments
4817 jmc 1.892 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
4818 mlosch 1.888 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
4819 mlosch 1.887 o add new diagnostics to seaice: advective, diffusive fluxes (only for
4820     multidim-advection, for scheme 2 they are not filled) and transports,
4821     thermodynamic growth rates
4822 jmc 1.902 o change units of EmPmR (inside the code, + within coupling interface)
4823     from m/s to kg/m2/s (mass flux) but leave input file unchanged.
4824     Affects results @ truncation level (cg2d match) and update output of
4825     experiments: lab_sea(6), global_ocean.90x40x15(10),
4826 jmc 1.886 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
4827     + adjoint results: global_ocean_ebm(11) and lab_sea (12).
4828 jmc 1.902 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
4829 jmc 1.886 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
4830    
4831 jmc 1.1203 checkpoint59h (2007/09/29)
4832 mlosch 1.884 o pkg/exf:
4833     - improve vectorization by moving if-statement out of loops in
4834     exf_mapfields, exf_radiation
4835     - exf_bulkformulae.F: introduce 2D fields and vectorize code
4836 dimitri 1.881 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
4837 jmc 1.880 o testreport:
4838     - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
4839     monitor & update offline_exf_seaice exp. output.
4840     - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
4841 mlosch 1.879 o pkg/seaice:
4842     - bug fix in the evp solver: boundary conditions were affected be
4843     masking of zMax/zMin (changes results)
4844     - minor bug fix in boundary conditions in seaice_calc_strainrates
4845     (changes results for no_slip)
4846     - seaice_lsr.F: make interpolation of eta dependent on boundaries
4847     - replace hardcoded lower limit for zeta (zMin) by runtime parameter
4848     - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
4849     stress formulation and no-slip boundary conditions
4850 jmc 1.878 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
4851     in gad_calc_rhs.F ; add few safety stops in initialisation phase.
4852 dimitri 1.877 o pkg/seaice: a first HSALT time stepping equation has been checked in
4853 dimitri 1.875 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
4854     in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
4855     without requiring DO-IF statements
4856 jmc 1.876 o pkg/thsice:
4857     use continuous power-law function for partition of energy between lateral
4858     melting/freezing and thinning/thickening ; old code using step function
4859     still available with #undef THSICE_FRACEN_POWERLAW
4860     update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
4861     o testreport: change AD testing : check against results/output_adm.txt
4862     using same scripts as for forward test.
4863 dimitri 1.875
4864 jmc 1.1203 checkpoint59g (2007/09/17)
4865 jmc 1.873 o adjoint testing: in preparation for changing testreport:
4866     - output format: cost and grad written on separated lines
4867     - ad output results in directory "results" (instead of "results_ad")
4868 dimitri 1.872 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
4869 dimitri 1.871 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
4870 gforget 1.870 o pkg/ecco: allow user defined cost function contributions
4871 jmc 1.869 o testreport:
4872     Allow to choose (per experiment) the list of tested output variables
4873     and the main variable (used to issue a pass/FAIL ) ;
4874     - for now, done by adding the specific list in file: [exp]/input/tr_checklist
4875 jmc 1.873 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
4876 jmc 1.869 Also modify printing of summary:
4877     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
4878     b) echo the list of tested variables in the individual summary.txt of
4879     each experiment.
4880 jmc 1.868 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
4881     threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
4882     (but still depend on the tile decompostion of the domain).
4883 mlosch 1.867 o pkg/seaice: change a discretization detail to make the B-grid code
4884     "more symmetric". This change is likely to remove all "ridges/leads" that
4885     where quasi-aligned with the grid in B-grid solutions. It may also be
4886     the solution to the stress coupling issues with the B-grid.
4887 jmc 1.866 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
4888     remove .cvsignore from input dir. (since testreport no longer run here).
4889 jmc 1.865 o pkg/thsice:
4890 jmc 1.866 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
4891 jmc 1.865 - fix reshaping of sea-ice just after advection:
4892     melt all the ice only if ice-volume is too small.
4893     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
4894     prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
4895     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
4896 jmc 1.864 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
4897     tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
4898 jmc 1.863 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
4899     forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
4900     (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
4901     and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
4902     of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
4903     -> update output.txt
4904     o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
4905     this affects truncation error: -> update output.txt of exp:
4906     global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
4907     ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
4908    
4909 jmc 1.1203 checkpoint59f (2007/08/21)
4910 gforget 1.861 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
4911     o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
4912     a bounded range (in forward mode)
4913 gforget 1.860 o pkg/ecco, ctrl, autodiff and mom_common:
4914     internal parameter controls, completements of implementations
4915 jmc 1.859 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
4916 jmc 1.862 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
4917     (not seem any difference in testing results).
4918 jmc 1.859 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
4919     at face corners.
4920 jmc 1.858 o pkg/generic_advdiff:
4921     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
4922     loop range indices for computing vertical advection tendency
4923     and do the calculation in the interior only (no overlap) ;
4924     for now, only implemented for SOM advection (to save CPU time).
4925     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
4926 heimbach 1.855 o exch2 adjoint
4927     First set of changes:
4928     - add exch2 hand-written adjoint templates
4929     - exch2 hand-written no longer use TAF-flag 'nownew_arg'
4930     This will require cleanup in pkg/autodiff/*.F
4931     (changed routines currently kept separate in verif. code/)
4932     - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
4933     that used to hide exch2 or cubed-sphere specific code
4934     (commented via 'cph-exch2')
4935 dimitri 1.856 o pkg/seaice
4936     - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
4937 jmc 1.857 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
4938     output of global_ocean.cs32x15.thsice .
4939 heimbach 1.855
4940 jmc 1.1203 checkpoint59e (2007/07/26)
4941 jmc 1.853 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
4942     for B-grid vector (not yet tested) and C-grid vector (<- only used
4943     when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
4944 dimitri 1.852 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
4945     (#ifdef ALLOW_SALT_PLUME)
4946 dimitri 1.851 o gather_2d/scatter_2d: removed halo regions
4947 jmc 1.845 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
4948     scheme and the corresponding test case (under front_relax dir). For now,
4949     only available with Skew-flux form and not yet tested in realistic set-up.
4950 heimbach 1.847 adjoint: store directives updated, but gradient checks deteriorated,
4951     so maybe GM/Redi adjoint is now broken.
4952 heimbach 1.844 o seaice adjoint
4953     * add AREA, HEFF, HSNOW as control variable
4954     (should not change lab_sea results)
4955     * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
4956 dimitri 1.848 o pkg/seaice:
4957     * added computation of saltFlux in seaice_growth;
4958     For time being, sea ice salinity is assumed constant
4959     contribution of snow flooding to freshening of sea ice is neglected.
4960     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
4961     defaults to 0.0 in order to maintain backward compatibility.
4962     Typical values for SEAICE_salinity are 4 to 10 g/kg.
4963     * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
4964     * added SEAICE_availHeatFrac, which specifies fraction of surface level
4965     heat content used to melt or grow ice
4966 dimitri 1.849 * commented out cap of HICE: it helps keep ice thinner
4967     * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
4968 dimitri 1.850 * applied OBCS T/S mask to HEFFM sea ice mask
4969 heimbach 1.844
4970 jmc 1.1203 checkpoint59d (2007/06/21)
4971 jmc 1.842 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
4972     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
4973     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
4974     o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
4975     and change default value of parameter "GM_Small_Number";
4976     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
4977     global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
4978     tutorial_global_oce_biogeo, tutorial_global_oce_latlon
4979 gforget 1.841 o pkg/ecco: cost function when applying pkg/smooth to controls
4980     o pkg/ctrl: add forcingPrecond run time parameter
4981 mlosch 1.839 o pkg/seaice:
4982     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
4983     - fix bug in metric terms of u-equation in LSR solver (implicit part),
4984     changes verification/lab_sea
4985     - rearrange implicit part of u-equation in LSR solver to make it easier to
4986     read, understand, and debug. This causes changes at the truncation level.
4987     - fix (serious) bug in the boundary conditions (sign error in the implicit
4988     part) of the LSR solver. Changes all LSR results.
4989 dimitri 1.840 - fixed problem with HSNOW initialization to avoid thick snow when AREA
4990     is initilized with small values - does not change lab_sea results.
4991     - added HsnowFile initialization capability
4992 gforget 1.838 o pkg/smooth: addition to model/src and pkg/ctrl so allow
4993     initialization of pkg/smooth and application to control vector
4994 mlosch 1.837 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
4995 gforget 1.836 o dependencies: pkg/profiles requires pkg/cal
4996 gforget 1.835 o pkg/profiles:
4997     - added option ALLOW_PROFILES_GENERICGRID
4998     -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
4999     that interpolation information (grid points and coefficients) is provided
5000     within the netcdf input files.
5001     -> sample matlab scripts can be found in MITgcm_contrib/gael
5002     that allow you to prepare netcdf input files.
5003     - also modified: cleaner include statements, cleaner error print statements,
5004     cleaner stops when error, and more tests of the netcdf input files consistency.
5005 jmc 1.834 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
5006 mlosch 1.830 o pkg/seaice:
5007 mlosch 1.833 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
5008     requires a new routine: seaice_diagnostics_fill.F
5009 mlosch 1.832 - make sure that seaice does not move if not forced (pressure replacement
5010     method, Hibler and Ip, 1995), changes results
5011 mlosch 1.830 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
5012     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
5013     It is turned off by default (=-1.), because it changes the results.
5014 mlosch 1.831 - make it possible to read AREA from a file, too.
5015 mlosch 1.830
5016 jmc 1.1203 checkpoint59c (2007/06/04)
5017 jmc 1.828 o add S/R and diagnostics for oceanic mixed-layer depth
5018     o move GMRedi call after all vertical mixing schemes (including KPP)
5019     o pkg/thsice:
5020     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
5021     (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
5022 mlosch 1.824 o pkg/obcs:
5023     - bug fix for balance code
5024 mlosch 1.822 o pkg/seaice:
5025 mlosch 1.825 - allow values of SEAICE_elasticParm > 1
5026 mlosch 1.826 - add new parameter SEAICE_evpTauRelax as an alternative
5027     to SEAICE_elasticParm
5028 mlosch 1.825 - make lsr boundary conditions free slip (by default), changes result
5029 mlosch 1.823 - add code for no slip boundary conditions for lsr
5030 mlosch 1.822 - set minimum of zeta to zero (and not 4e8) (changes results)
5031 mlosch 1.826 - add a cap on AREA after advecting AREA if seaice_growth is not called
5032 jmc 1.821 o change calculation of Visbeck K:
5033     - no longer depend on tapering scheme; instead, compute slope (limited
5034     by GM_maxSlope). this is equivalent to what was comuted before with
5035     clipping or linear tappering.
5036 jmc 1.828 - fix vertical averaging (wrong by 1/2 level)
5037 jmc 1.821 - leave the old version (but will not be maintained) within
5038     #ifdef OLD_VISBECK_CALC / #endif
5039 jmc 1.828 - update output of exp. ideal_2D_oce
5040 mlosch 1.820 o change error catch in calc_r_star to improve vectorization
5041 jmc 1.819 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
5042     add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
5043 heimbach 1.827 o adjoint:
5044     Re-organized adjoint checkpointing according to Matt Mazloff
5045     (but with modifs/completions/cleanups)
5046     Storing is now bundled into large arrays to optimized I/O
5047     (and second step in cleanup of the_main_loop)
5048 jmc 1.819
5049 jmc 1.1203 checkpoint59b (2007/05/16)
5050 jmc 1.818 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
5051     - export/import (between ocean & coupler) fields needed for ocean DIC.
5052 mlosch 1.817 o pkg/seaice:
5053     - get rid of three more exchanges seaice_calc_viscosities (required
5054     different loop boundaries in seaice_lsr and seaice_ocean_stress)
5055     - bug fix in seaice_ocean_stress (update of lab_sea required)
5056     - reduce loop boundaries to necessary minimum also in seaice_evp
5057     - go back to the old way of computing deltaC/Z as the adjoint likes that
5058     better
5059 dfer 1.816 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
5060     passive tracer to an Age Tracer) + update output.txt
5061 jmc 1.814 o pkg/exf:
5062 jmc 1.815 - implement A-grid / C-grid selection for wind-stress input files.
5063     - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
5064     for now, in exf_bulk_largeyeager04.F only :
5065     - change implementation for case where windspeed + 2. components wind-stress
5066     are read-in. AND use rhoConstFresh to convert evap.
5067     o pkg/seaice:
5068     - use correct EXCH_UV for wind-forcing (on A-grid).
5069     - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
5070     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
5071     o pkg/exf:
5072 jmc 1.814 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
5073     EXF_INTERPOLATION:
5074     - merge global_with_exf/code version of exf_interp_read.F
5075     to the main code ;
5076     - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
5077     reading the file ; Important: This options needs to be defined to recover
5078     previous code.
5079     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
5080     - no longer loose real*8 precision along the way when using exf_iprec=64.
5081 mlosch 1.811 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
5082 mlosch 1.813 - change discretisation of evp-solver in order to avoid another exchange
5083     (changes lab_sea) and clean up a little
5084     - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
5085     help the adjoint (this also changes the results slightly)
5086     - add a few "_d 0" where they had been missing in seaice_evp.F
5087     - cleaning up: remove unused seaice_calc_rhs.F
5088 jmc 1.810 o pkg/exf: some cleaning-up:
5089     - change various "constants" into runtime parameters
5090     - cleaned-up Large&Yeager04 routine which should eventually
5091     replace exf_bulkformulae.F (changed names of S/R and CPP)
5092     and merged various ALLOW_ATM_WIND options
5093     only used with thsice pkg (in thsice_get_exf.F):
5094     - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
5095     which are used when useStabilityFct_overIce=TRUE (= the default)
5096     - change default values of ice & snow emissivity and scale downward LW
5097     by ice & snow emissivity.
5098     o pkg/thsice:
5099 jmc 1.809 fix few little problems, in thsice_calc_thickn.F:
5100     - growth vertically (and not laterally) if iceFrac == iceMaskMax
5101 jmc 1.828 - melt only laterally if hIce < hThinIce (as the comments say)
5102 jmc 1.809 and in thsice_extend.F:
5103     - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
5104     - start to form ice as soon as the minimum ice-volume is reachable.
5105     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
5106     and cpl_aim+ocn
5107 mlosch 1.807 o pkg/kpp
5108 jmc 1.809 - move computation of surface related input fields to KPP into a new
5109     subroutine kpp_forcing_surf.F
5110 jmc 1.808 - remove wrong (within bi,bj loops) EXCH calls.
5111     - little cleaning (add argument myThid in last position, cvs header ...)
5112 jmc 1.809 - for now, fix conservation problem by exchanging KPPviscAz (may not
5113     be the best fix)
5114 mlosch 1.806 o pkg/seaice
5115     - check for inconsistent evp parameter/cpp-flag combination
5116     - remove leftover errIO flat for obsolete name list error handling
5117 heimbach 1.812 o OpenAD
5118     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
5119 mlosch 1.806
5120 jmc 1.1203 checkpoint59a (2007/05/01)
5121 mlosch 1.803 o pkg/seaice: some parameter clarifications and a little bit of clean up
5122 jmc 1.802 o pkg/thsice: rename run-time parameters:
5123     himin -> hIceMin
5124     himin0 -> hThinIce
5125     hihig -> hThickIce
5126     i0 -> i0swFrac
5127     transCoef -> bMeltCoef
5128     frac_energy -> fracMelting
5129     add new parameters: hNewIceMax, fracFreezing, dhSnowLin
5130     with default values (for now) that do not change the results.
5131     remove old version of thsice vars advection in pkg/seaice.
5132 jmc 1.801 o in FFIELDS.h:
5133     - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
5134     - make pLoad & sIceLoad always available (but still only used if
5135     ATMOSPHERIC_LOADING is #define).
5136 dimitri 1.799 o pkg/kpp: replaced _KPP_RL with _RL
5137 dimitri 1.798 o bug fixes for vertical diffusivity computations when both KPP and
5138 dimitri 1.883 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
5139     are no longer updating the vertical diffusivity array
5140     (passed as argument) but are (re-) setting those arrays.
5141 mlosch 1.795 o pkg/seaice: fix bug in evp solver, while doing that
5142     - change (improve?) discretization of stress computations for both
5143     cgrid-lsr and evp solver
5144     - add a new routine to compute strain rates
5145 mlosch 1.796 - the above changes lab_sea results
5146     - add no slip conditions for evp solver (off by default), lsr-version
5147     may follow
5148     - fix exchange for shear at Z-points (does not change lab_sea)
5149     - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
5150     (to force the user to pick a time step since there is not "safe" way
5151     of choosing it)
5152 mlosch 1.797 - add principal stress diagnostics
5153 mlosch 1.800 - rearrange fields for evp a little to avoid having to call a: too many
5154     exchanges and b: exchanges for stress trensor components which we do
5155     not have.
5156     - modify Hibler+Bryan (1987) stress coupling so that it reuses information
5157     of evp, complete rewrite for lsr case (latter is does not yet work
5158     in all cases)
5159 mlosch 1.794 o pkg/kpp: add code to have mixing in shelf ice caverns
5160 mlosch 1.804 - add myThid to all kpp routines (long overdue)
5161 mlosch 1.794
5162 jmc 1.1203 checkpoint59 (2007/04/19)
5163 heimbach 1.792 o pkg/exf:
5164     - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
5165     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
5166     - move exf header files from lower_case.h to UPPER_CASE.h ;
5167     add missing cvs Header & Name
5168     - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
5169 heimbach 1.793 - add namelist param. selectStressGridPosition, exf_monFreq
5170     - retire many _CLIM routines, and remove data.exf_clim
5171     + params moved to data.exf
5172     + climsst, climsss now handled by exf_set_gen, i.e.
5173     climss?period=0 refers to constant field,
5174     climss?period=-12 to monthly forcing
5175     - split up namelists in data.exf
5176 mlosch 1.788 o pkg/seaice:
5177     - remove seaice_exch and seaice_exch_uv
5178     - remove superfluous exchange of theta
5179     - add myThid to seaice_budget_ocean/ice
5180 mlosch 1.790 - add new interface for atmospheric wind forcing (C-grid only)
5181     + new routine
5182     + two new field (taux, tauy for stress over ice)
5183     + removed one global field (DAIRN) for C-grid case only
5184 heimbach 1.792 o pkg/thsise
5185     - 2nd set of modifs for thsice adjoint in conjunction with exf
5186 heimbach 1.793 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
5187 mlosch 1.788
5188 jmc 1.1203 checkpoint58y_post (2007/04/15)
5189 dimitri 1.785 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
5190 dimitri 1.786 vertical diffusivity, similar to that in MOM4; turned on using
5191     #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
5192     diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
5193 dimitri 1.782 o Added capability for 3D specification of background vertical diffusion
5194     coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
5195     in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
5196     "data" file that contains the 3D vertical diffusivity coefficients.
5197 jmc 1.784 o ice dynamics (pkg/seaice) with thsice thermodynamics:
5198     - add code within pkg thsice to advect & diffuse sea-ice fields
5199     similar to (and will replace) what has been added in seaice_advdiff.F,
5200     but: - conserving Mass, Heat & Salt.
5201     - better when using non-linear advection scheme (not yet fully tested)
5202     - can also be used in atmospheric set-up (for now, only the diffusion).
5203 dimitri 1.783
5204 jmc 1.1203 checkpoint58x_post (2007/04/04)
5205 jmc 1.779 o IO option for global-file compact format:
5206     - add options when generating topology (utils/exch2/matlab-topology-generator)
5207     - add I/O capability (pkg/mdsio).
5208     - adapt utils/matlab/rdmds.m to read this format.
5209     for now long-line format not yet supported by pkg/mdsio (& exch2).
5210 mlosch 1.778 o shelfice: add a few diagnostics
5211    
5212 jmc 1.1203 checkpoint58w_post (2007/03/13)
5213 jmc 1.776 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
5214     rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
5215     (and replace horiVertRatio in NH code).
5216     Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
5217     and tutorial_plume_on_slope (sensitive to truncation)
5218 mlosch 1.774 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
5219     directly to drive seaice model (C-grid only)
5220     o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
5221     - reintroduce computation of wind from stress,
5222     - compute tau (in exf_bulkformulae.F) from windstress averaged to
5223     mass points to avoid tau = 0
5224 mlosch 1.775 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
5225 mlosch 1.774 o rdmnc.m: make it work with "global" files created with gluemnc
5226 jmc 1.773 o rdmnc.m : some improvements in dealing with singleton dimension
5227     (tested on all testreport mnc output files).
5228     o genmake2: disable pkg/profiles if netcdf test fails.
5229 jmc 1.772 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
5230 mlosch 1.771 o move call to cal_readparms up to make calendar parameters/variable available
5231     to all packages
5232    
5233 jmc 1.1203 checkpoint58v_post (2007/02/08)
5234 jmc 1.770 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
5235     useDynP_inEos_Zc tested.
5236 dimitri 1.769 o pkg/exf: changes to properly interpolate/mask/scale initial fields
5237 dimitri 1.768 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
5238     and portions thereof. See read_cs.txt for description and examples.
5239 jmc 1.767 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
5240     add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
5241     following the great-circle arc between those 2 points.
5242     o trap un-initialized variable with pathscale compiler on weddell.mit.edu
5243     (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
5244 jmc 1.766 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
5245     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
5246     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
5247     - still needs work (not working with some options ; efficiency to improve)
5248     and serious testing.
5249     - use this scheme for temperature & salinity in 2 advection test exp.:
5250     advect_xy & advect_xz, respectively.
5251    
5252 jmc 1.1203 checkpoint58u_post (2007/01/12)
5253 jmc 1.765 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
5254 jmc 1.764 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
5255     o testreport: add option "-skipdir" to skip some test.
5256     o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
5257     momentum calculation.
5258     o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
5259     o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
5260     remove checkpoint.F and the_correction_step.F (no longer used);
5261     do the k loop inside CYCLE_TRACER (supposed to be more efficient).
5262     o add option (linFSConserveTr) to correct for tracer source/sink due to
5263     Linear Free surface
5264 mlosch 1.763 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
5265     o pkg/thsice: fix reading mnc-pickups
5266    
5267 jmc 1.1203 checkpoint58t_post (2006/12/30)
5268 jmc 1.761 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
5269     o pkg/mdsio:
5270     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
5271     move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
5272     mdsio_write_field.F (S/R MDS_WRITE_FIELD);
5273     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
5274     - collect old S/R in one file: mdsio_rw_field.F (now just a call to
5275     either MDS_READ_FIELD or MDS_WRITE_FIELD )
5276     - new S/R (to replace MDSWRITEMETA), which allows to write more
5277     informations (variable names, time ...) to meta files.
5278     - modify rdmds.m to give back the meta file content.
5279 jmc 1.760 o pkg/diagnostics: change vertical interpolation to be safer, and more
5280     flexible (define p-levels to interpolate to in data.diagnostics);
5281     add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
5282     diagnostic pointer.
5283 mlosch 1.759 o pkg/seaice: more cleaning up of seaice_growth, added many comments
5284 mlosch 1.763 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
5285 mlosch 1.757 o fix multi-category seaice:
5286     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
5287     SEAICE_MULTICATEGORY
5288     - fix short wave heat flux
5289 jmc 1.758 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
5290     and allow to use EVP solver. Change forward lab_sea: test both EVP
5291     solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
5292 heimbach 1.756 o Initial check-in of lab_sea adjoint
5293     (very similar to natl_box_adjoint/code_seaice)
5294     * used C-grid and EVP solver
5295     * used KPP, GM/Redi
5296     * uses inAdExact=.TRUE.
5297     * gradient checks fail for both ADM and TLM
5298     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
5299     f.d. gradients actually seem more problematic than ADM, TLM gradients;
5300     issue is related to forward mismatch between g77 an ifort
5301 mlosch 1.755 o pkg/seaice: overhaul of thermodynamics
5302     - growth.F and groatb.F are replaced by new routine seaice_growth.F
5303     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
5304     - move a few global fields out of SEAICE.h into seaice_growth.F and
5305     make them 2D (FICE/QNETO/ ...)
5306     - remove FO (it is the same as QNETO)
5307     - introduce a few local fields to avoid modifying external fields such
5308     as atemp, etc.
5309    
5310 jmc 1.1203 checkpoint58s_post (2006/12/11)
5311 dimitri 1.753 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
5312     changed exf_set_gen.F so that
5313     genperiod=0 means input file is one time-constant field and
5314     genperiod=-12 means input file contains 12 monthly means
5315 jmc 1.752 o CG2D: use pre-computed solver main-diagonal (stored in common block);
5316     this affects truncation error ; generate new output file for exp. which
5317     fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
5318     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
5319     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
5320     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
5321     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
5322     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
5323 jmc 1.751 o start implementation of deep-atmosphere and anelastic formulation
5324 jmc 1.750 o verification: remove 2nd copy of input files and use script "prepare_run"
5325     to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
5326 mlosch 1.749 o mom_common/vecinv/fluxform: fix a few initialisation isssues
5327 gforget 1.748 o profiles: fix for multithreaded case
5328    
5329 jmc 1.746 o diagnostics: rename few diags:
5330     s/'PRESSURE'/'RCENTER '/g
5331     s/'TICE '/'oceFreez'/g
5332     s/'TAUX '/'oceTAUX '/g
5333     s/'TAUY '/'oceTAUY '/g
5334     s/'SWFLUX '/'oceQsw '/g
5335     s/DIFx/DFxE/g
5336     s/DIFy/DFyE/g
5337     and add few ocean-forcing diagnostics:
5338     atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
5339 dimitri 1.747 o modifications to pkg/seaice/growth.F and budget.F, which change results of
5340     lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
5341     as actual snow thickness. It now refers everywhere to effective snow
5342     thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
5343 jmc 1.746
5344 jmc 1.1203 checkpoint58r_post (2006/11/17)
5345 dimitri 1.744 o modifications to pkg/seaice/growth.F, which change results of
5346     lab_sea experiment: fixes pertain to melting snow over open water, to
5347     masking EVAP under sea ice, and to using the correct AREA variable for
5348     computations of EVAP, PRECIP, HSNOW, and GHEFF
5349 edhill 1.743 o add ability to read bathy, salt, and theta using MNC (off by def)
5350 mlosch 1.742 o add flooding algorithm and advection of HSNOW for pkg/seaice;
5351     both are turned off by default and do no change any results
5352 jmc 1.741 o seaice advection with pkg/thsice: a step toward the use of non-linear
5353     advection scheme, but #ifdef or commented out for now (requires more EXCH).
5354 jmc 1.739 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
5355     (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
5356     in natl_box (affects results @ truncation level: update output.txt)
5357     o multi-threading and IO:
5358 jmc 1.738 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
5359     - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
5360     (needed to work with SingleCpuIO): tested in all verif. exp.
5361 jmc 1.737 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
5362     affects the results (but none of the verification test uses this scheme).
5363 heimbach 1.736 o Adding some pkg/diagnostics capability to pkg/seaice
5364     (will certainly be subject to changes)
5365 heimbach 1.740 o ctrl: adding new control variables:
5366     lwflux, lwdown, evap, snowprecip, apressure, runoff
5367 heimbach 1.736
5368 jmc 1.1203 checkpoint58q_post (2006/10/20)
5369 dimitri 1.734 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
5370     1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
5371     high_res_cube configuration by 4% on Columbia.
5372 jmc 1.733 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
5373     add (in global_with_exf/code) a version of EXF_INTERP_READ without
5374     dynamical allocation (seems to work in multi-threaded).
5375     o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
5376     single CPU io) so that TAF does not have to see EESUPPORT.h
5377 jmc 1.727 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
5378    
5379 jmc 1.1203 checkpoint58p_post (2006/09/08)
5380 mlosch 1.726 o obcs: stop if obcs is used with useCDscheme = .true.
5381 mlosch 1.723 o shelfice:
5382     - fix a sign error so that no slip at shelfice interface works
5383     - remove stop for combination non-hydrostatic code and shelfice. That does
5384     not mean, that the results are correct, but at least they are numerically
5385     stable
5386 dfer 1.721 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
5387 heimbach 1.724 o added adjoint exch routined for all exch*3d* routines
5388     and updated flow directives
5389 dfer 1.721
5390 jmc 1.1203 checkpoint58o_post (2006/08/28)
5391 jmc 1.720 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
5392     remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
5393 jmc 1.719 o change controling S/R for writing pickup file (new S/R do_write_pickup)
5394     and clean-up reading/writing of pickup files.
5395     o fix local version of read/write pickup (NH part) in rotating_tank/code
5396 jmc 1.718 o simplify EXCH interface:
5397     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
5398     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
5399 edhill 1.717 o added the regrid package
5400 mlosch 1.716 o shelfice:
5401     - add a simple boundary layer scheme to reduce noise
5402     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
5403 jmc 1.718
5404 jmc 1.1203 checkpoint58n_post (2006/08/14)
5405 jmc 1.713 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
5406     local variable (not in common block).
5407 jmc 1.712 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
5408     - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
5409     - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
5410     to work with SingleCpuIO.
5411 jmc 1.711 o add "_d 0" to real constant of pkg/cfc subroutines ;
5412     update exp. cfc_exemple & tutorial_cfc_offline output files.
5413 jmc 1.710 o multi-threading and IO:
5414     - all threads call READ_FLD S/R (needed if using SingleCpuIO):
5415     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
5416     - barrier before and after reading.
5417     - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
5418     - avoid using MDS_WRITELOCAL for LAND pkg output.
5419     - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
5420     common-block variables ; Allows multi-threading with master-thread IO.
5421 jmc 1.709 o change default MAX_NO_THREADS from 32 to 4 ;
5422     and stop cleanly when MAX_NO_THREADS is too small.
5423     o add S/R BAR_CHECK to check multi-threaded barrier synchronization
5424    
5425 jmc 1.1203 checkpoint58m_post (2006/07/17)
5426 jmc 1.707 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
5427     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
5428 jmc 1.706 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
5429     keep global_ocean.90x40x15 (for AD testing) with former secondary test
5430     (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
5431     o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
5432     add MITgcm_tutorials (= code + all the tutorials)
5433 gforget 1.705 o ecco, option to compute cost for total ssh (mean+anom)
5434 gforget 1.704 o consistent with addition of ptracer and ssh in pkg/profiles
5435 gforget 1.703 o profiles: adding ptracer and ssh
5436 jmc 1.702 o testreport: change multi-test output-file name
5437     (from output.txt.{name} to output.{name}.txt)
5438 jmc 1.712 o profiles: now ok for mutli-tiles case
5439 mlosch 1.700 o seaice: add 4 parameters for different advection schemes for area,
5440     (effective) seaice thickness, enthalphy, and snow height. Their default
5441     is the standard parameter SEAICEadvScheme
5442 jmc 1.699 o calc_gw:
5443     - add cosFacU in zonal viscous flux (harmonic.visc.).
5444     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
5445     of tutorial_plume_on_slope.
5446     o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
5447 jmc 1.698 o calc_gw: true flux-form, account for horizontal grid spacing.
5448     update rotating_tank results, but not plume_on_slope (affected at
5449     truncation level, 11 digits).
5450    
5451 jmc 1.1203 checkpoint58l_post (2006/07/12)
5452 jmc 1.698 o calc_gw:
5453     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
5454     - remove side-drag for now (need to fix it); update plume_on_slope results.
5455     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
5456 heimbach 1.695 o commit code to make SST/SSS weights spatially variable
5457     (based on either variable in-situ or variable initial T/S weights)
5458 heimbach 1.696 o pkg/ecco:
5459     * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
5460     now based on horizontally varying weights wthetaLev, wsaltLev
5461     * cost_averagesflags now returns year indices in addition to day, month
5462     * sflux balance is performed on annual basis
5463     (sflxumm, sfluxmm2, bal_sfluxmm)
5464     * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
5465     including separate counting and multipliers
5466 heimbach 1.697 o pkg/rbcs
5467     * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
5468 jmc 1.694
5469 jmc 1.1203 checkpoint58k_post (2006/07/06)
5470 jmc 1.692 o testreport:
5471     - always build in dir. "build" (if not there, mkdir build instead of building
5472     & running in input)
5473     - run in dir run (if it exists), in build otherwise.
5474     - call prepare_run (if input/prepare_run exists)
5475     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
5476 dimitri 1.691 o pkg/exf modifications to interpolation and rotation routines for more
5477     reasonable treatment of North Pole singularity: for tracers North Pole
5478     value is set to northernmost zonal-mean value, for zonal velocity it is
5479     set to zero, and for meridional velocity it is set to northernmost value.
5480 mlosch 1.690 o pkg/exf/exf_check_range.F
5481     - add tile index to diagnostics and move stop statement to the very
5482     end of the routine.
5483 jmc 1.689 o pkg/diagnostics: (diagnostics_main_init.F)
5484     define title of isomorphic variables according to the current config.
5485 jmc 1.687 o pkg/thsice with pkg/seaice dynamics:
5486 jmc 1.688 - fix domain of computation (interior only, required for exf) and do exchanges
5487     - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
5488 jmc 1.686 o towards a standard way of dealing with multi-threading in MONITOR
5489     and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
5490 baylor 1.685 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
5491     to W momentum equation in nonhydrostatic and quasihydrostatic runs.
5492 jmc 1.684 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
5493 jmc 1.683 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
5494     o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
5495     (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
5496 jmc 1.682 o tracer advection:
5497     - clean-up and simplify calc_common_factors.F
5498     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
5499     advection subroutine (but still not used within DST advection S/R)
5500 jmc 1.681 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
5501    
5502 jmc 1.1203 checkpoint58j_post (2006/06/15)
5503 heimbach 1.680 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
5504     from file (collects calls previously in FORWARD_STEP)
5505     o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
5506 heimbach 1.679 o adjoint store dir. adjusted accordingly
5507 heimbach 1.680 o genmake2
5508     replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
5509 heimbach 1.679
5510 jmc 1.1203 checkpoint58i_post (2006/06/14)
5511 mlosch 1.677 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
5512     on wind stress (SEAICEstressFactor defaults to 1.)
5513 jmc 1.676 o Total number of Timers is finite (<=40): comment out 2 non-essential one
5514     in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
5515 jmc 1.675 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
5516     on CS-grid: no longer loosing mass.
5517 jmc 1.674 o exf & curvilinear-grid: no longer modify longitude xC & xG.
5518 mlosch 1.670 o pkg/ggl90: fix sloppy output and fix a bug
5519 dimitri 1.672 o pkg/seaice: added SEAICEuseEVPpickup parameter
5520     - Set to false in order to start EVP solver with
5521     non-EVP pickup files when using SEAICEuseEVP
5522 mlosch 1.673 - fix sign error in diffusion in seaice_calc_rhs
5523 mlosch 1.670
5524 jmc 1.1203 checkpoint58h_post (2006/06/07)
5525 heimbach 1.669 * Modifications for bottom topography control
5526     o replace hFacC by _hFacC at various places
5527     o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
5528     o add non-self-adjoint cg2d_nsa
5529     o update autodiff support routines
5530     o re-initialise hfac after ctrl_depth_ini
5531     o works for 5x5 box, doesnt work for global_ocean.90x40x15
5532     * Adding verification for 5x5 box (4-layer) bottom topography control
5533    
5534 jmc 1.1203 checkpoint58g_post (2006/06/07)
5535 jmc 1.671 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
5536     used for mean seasonal cycle, mean diurnal cycle); add an example
5537     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
5538 mlosch 1.667 o pkg/ggl90:
5539     - add parameter (minimum surface kinetic energy)
5540     - fix bug (avoiding division by zero)
5541 mlosch 1.665 o couple pkg/thsice to pkg/seaice:
5542     - modify advection in seaice to accomodate new scalar fields to be advected
5543     - only muliDimAdection scheme work with seaice/thsice
5544     - mapping of thsice-variables to seaice-variables, back and forth
5545     - does not break the verification experiments, but does not give the
5546     desired results either
5547     o pkg/seaice
5548     - make (default) second order advection a bit less confusing?
5549    
5550 jmc 1.1203 checkpoint58f_post (2006/06/05)
5551 mlosch 1.662 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
5552     to pkg/seaice):
5553     - new routines thsice_map_exf and thsice_get_exf provide the interface
5554     - add an additional formal parameter to thsice_solve4temp
5555 heimbach 1.661 o pkg/exf:
5556     - add new fields wspeed, snowprecip (to be able to couple to thsice)
5557     - correct Stefan-Boltzmann constant
5558     - new parameter for longwave surface emittance
5559     - separate some stuff from exf_bulkformulae into new routines
5560     exf_radiation, exf_wind
5561 mlosch 1.662 - add new parameters and constants: longwave emissivity for ocean, ice
5562     and snow, evaporation parameters over ice
5563 mlosch 1.663 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
5564     either wind from stress or stress from wind
5565 jmc 1.660 o pkg/thSIce:
5566     - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
5567     - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
5568     and THSICE_CALC_THICKN
5569     - for now, call to THSICE_GET_BULKF remains inside i,j loops.
5570     - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
5571     to make debugging easier.
5572     - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
5573     o pkg/bulk_force:
5574     - clean-up comments and parameters ;
5575     - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
5576 jmc 1.659 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
5577     generate new output for test-experiment: aim.5l_cs.thSI
5578 jmc 1.658 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
5579 heimbach 1.661 testreport accordingly
5580 jmc 1.658
5581 jmc 1.1203 checkpoint58e_post (2006/05/17)
5582 heimbach 1.656 o SEAICE_CGRID adjoint done
5583 heimbach 1.654 o R_STAR adjoint implemented.
5584     * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
5585     * need to sort out init. of h0facc, etc.
5586 heimbach 1.655 o Make pkg/profile fully independent of ecco,cost, etc. stuff
5587     to be able to use it in pure forward.
5588 heimbach 1.653
5589 jmc 1.1203 checkpoint58d_post (2006/04/21)
5590 jmc 1.651 o upgrade simple test-experiment to tutorial example:
5591     step.1: duplicate the experiment and (step.2) will remove the old copy.
5592     tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
5593     tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
5594     tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
5595     tutorial_global_oce_biogeo <- copy of dic_example
5596     tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
5597     tutorial_plume_on_slope <- copy of plume_on_slope
5598     tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
5599     tutorial_global_oce_optim <- empty for now (David ?)
5600     tutorial_global_oce_in_p <- copy of global_ocean_pressure
5601     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
5602 gforget 1.650 o correct a sign problem in cost_scat.F
5603 mlosch 1.649 o obcs and ptracers: fix boundary conditions for advections schemes
5604     with larger stencil
5605 heimbach 1.648 o thsice adjoint: start
5606 mlosch 1.647 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
5607     completeness
5608 mlosch 1.646 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
5609     and COSINEMETH_III, add comments in default CPP_OPTIONS.h
5610 heimbach 1.645 o ptracers adjoint:
5611     * avoid extensive recomputatations
5612     * fix missing re-init. of gptr (missed by TAF)
5613 mlosch 1.644 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
5614     me to turn off the excessive output to STDOUT that this package produces
5615 jmc 1.643 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
5616     and add those terms in Vector-Invariant formulation.
5617 gforget 1.642 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
5618     if the control period (xx_hfluxperiod etc) is 0
5619     o in profiles pkg, clean routines and fix details
5620     o in ecco pkg, reading ssh data:
5621     fix problem in case the model does not start at iter0=0
5622 mlosch 1.640 o fix mnc-pickup/restart for ptracers
5623 heimbach 1.641 o new package prifiles:
5624     code to compute profile-based cost by Gael Forget
5625 heimbach 1.639 (modifs in ecco, ctrl, autodiff)
5626 heimbach 1.641 o Benign bug fix in initialization (spotted by M. Mazloff) of
5627     ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
5628 heimbach 1.639
5629 jmc 1.1203 checkpoint58c_post (2006/03/23)
5630 heimbach 1.638 o adjoint: finish NLFS adjoint and provide reference output in
5631     verification/global_ocean.90x40x15/results_ad_nlfs
5632 mlosch 1.637 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
5633     documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
5634     SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
5635     with SEAICE_CGRID defined.
5636 jmc 1.636 o move calendarDumps from "data" to "data.cal" and clean-up the code
5637     with a simple call to pkg/cal S/R: CAL_TIME2WRITE
5638     o add useEXF & useCAL flags (for now, set in hard-coded way)
5639 jmc 1.635 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
5640     (were missing in NH mode, and wrong in quasihydrostatic mode).
5641     waiting for Chris updated version of calc_gw to add those CALLs.
5642     o fix bug in quasihydrostatic S/R ;
5643     add a test for this option: global_ocean.90x40x15.qshyd
5644 jmc 1.634 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
5645     (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
5646     o add on/off flag useOffLine for package OFFLINE
5647 mlosch 1.630 o seaice:
5648     - modify advection so that it works also on the C-grid
5649     - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
5650     problem in multi-tile runs with C-grid
5651 mlosch 1.633 - add flags for clipping ice velocities and/or masking solver forcing
5652 mlosch 1.631 - fix drag (ocean on ice) formulation and a bug that caused noise in the
5653     C-grid solver
5654 mlosch 1.632 - added a few comments to seaice_diffusion.F
5655     - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
5656     are now exclusive)
5657     - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
5658     required re-ordering the code a little:
5659     + make DAIRN global variable (defined in SEAICE)
5660     + move computation of the viscosities eta and zeta into a new separate
5661     routine (because I need to recompute them in seaice_ocean_stress.F)
5662 mlosch 1.629
5663 jmc 1.1203 checkpoint58b_post (2006/03/13)
5664 jmc 1.627 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
5665     update output.txt of exp. aim.5l_cs.thSI
5666 edhill 1.626 o various mnc cleanups and improvements:
5667     + shrink lookup tables by factor of ~4
5668     + better error reporting when running out of lookup space
5669     + able to handle longer path/file names (up to 500 chars)
5670 heimbach 1.625 o adjoint:
5671     - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
5672     - TBD: "hidden" mom_vecinv recomp. in dynamics
5673 jmc 1.624 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
5674     (allow to differentiate between forcing components using new integer flags:
5675     momForcingOutAB=1/0 & tracForcingOutAB=1/0)
5676     and add new flag to put Dissipation tendency out of Adams-Bashforth.
5677 heimbach 1.623 o ecco
5678     - enable trend removal from SSH anomaly obs.
5679     o adjoint
5680     - a fix for PmEpR when #undef EXACT_CONSERV
5681     - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
5682     - try to fix "hidden" recomp. in forward_step for NLFS
5683     (NLFS seems broken sometimes after I checked it in)
5684 mlosch 1.622 o seaice:
5685     - add c-grid version of the dynamic solver:
5686     + three new routines that are the c-grid substitute lsr, dynsolver
5687     and ostres
5688     + put a few fields that were local to dynsolver into global common
5689     blocks, so that I can move the computation of stresses etc into
5690     seaice_lsr (saves coding but may break the adjoint).
5691     - replace more hardwired parameters by runtime parameters
5692     - add ice masks that mask the rhs of the implicit solvers where there
5693     is no ice (commented out in seaice_dynsolver, because i am not sure
5694     if this works properly), eventually this should replace the clipping
5695     of ice velocities in seaice_dynsolver to +/-40cm/s.
5696 edhill 1.621 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
5697     include it only where its needed
5698 mlosch 1.620 o move balancing of fluxes before the call of external_forcing_surf
5699 mlosch 1.619 o seaice:
5700     - correct units of turning angles (now they are really in degrees)
5701     - move computation of GWATX/Y out of main routine into dynsolver
5702     - initialize GWATX/Y in seaice_init
5703 jmc 1.618 o Apply mask on Fresh-Water flux (needed for SSH forcing).
5704 mlosch 1.619 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
5705 mlosch 1.617 o seaice: add runtime flags for turning angles (default to zero)
5706 heimbach 1.616 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
5707     and trend from exf forcing and ctrl control adjustments
5708     o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
5709     (since checkpoint57x_post)
5710 jmc 1.615 o change the default rotation period to 86164.s = the Earth rotation
5711 jmc 1.614 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
5712     and based on a reference stratification. Tested within hs94.cs-32x32x5.
5713 mlosch 1.613 o seaice advection: add code for choosing between the default (2nd order
5714     central differences) and multiDim advection schemes provided by
5715     pkg/generic_advdiff
5716 mlosch 1.611 o seaice:
5717     - removed all references to SEAICE_GRID.h fields from
5718     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
5719     (cubed-sphere configuration will change a little)
5720     - grid computations in seaice_init are obsolete now.
5721     - cleaned up code a little so that is easier to read (hopefully).
5722 mlosch 1.613 - added new (better?) discretizations of default advection and diffusion
5723     (turn on with SEAICEuseFluxForm)
5724     - replace 1 in 3d global fields by kSurface in growth.F
5725 mlosch 1.611
5726 jmc 1.1203 checkpoint58a_post (2006/02/13)
5727 mlosch 1.612 o seaice:
5728     - bug fix in advect.F
5729 mlosch 1.608 o shelfice:
5730     - separate shelfice load anomaly from pload (breaks with time
5731     dependent forcing), => introduce constant field shelficeLoadAnomaly.
5732     Its default is 0., but it may be computed more cleverly from (unknown)
5733     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
5734     done offline. A good approximation of the pressure load anomaly is
5735     necessary to avoid large initial adjustment processes underneath
5736     deep-reaching shelfice.
5737 mlosch 1.609 - small fix in ISOMIP shelfice_thermodynamics
5738     - add more sophisticated thermodynamics of Hellmer (1989), this is
5739     now the default
5740     - give a few constants more intuitive names
5741 mlosch 1.607 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
5742     if bulk formulae are used in long integration (especially EmPmR). Turn
5743     on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
5744     if balancePrintMean, the imbalance that is substracted is printed to
5745     STDOUT.
5746 jmc 1.606 o fix bug (typo) in obcs_apply_eta.F
5747 mlosch 1.605 o add a new package shelfice which enables us to model the circulation
5748     underneath shelf-ice with draughts of hundreds of meters.
5749     - works
5750     - to do: + include improved thermodynamics
5751     + check whether kSurfC (from model/inc/SURFACE.h) can be used
5752     instead of new field kTopC
5753     + can we use topoFile, Ro_surf and existing code in ini_depth.F
5754     instead of new field R_shelfIce and new code in ini_depth.F
5755     and ini_mask_etc.F?
5756 mlosch 1.608 + adjust vertical mixing schemes?
5757 mlosch 1.604 o seaice pkg:
5758     - add a cpp-flag to include a simple formula for a salinity dependent
5759     freezing point of sea water at the surface
5760     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
5761     meridional stresses are now different (and hopefully correct)
5762 jmc 1.602 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
5763     update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
5764     and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
5765 jmc 1.601 o pkg/diagnostics: add options and parameters for regional-statistics
5766     diagnostics ; define regions by reading a region-mask from a file
5767     (might add other options later)
5768 jmc 1.600 o pkg/bulk_force:
5769     - add option and parameters to use AIM surface-flux formulae.
5770     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
5771     others forcing fields (defined in PARM05, parameter file "data") are loaded
5772     from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
5773     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
5774     - use the right EXCH call for uwind,vwind (to work on CS-grid).
5775     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
5776     and parameters (note: calcWindStress replaces .NOT.readwindstress).
5777     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
5778    
5779 jmc 1.1203 checkpoint58 (2006/01/12)
5780 edhill 1.598 o add "--embed-source" option to genmake2 which, when the supporting
5781     tools can be compiled (as determined by genmake2) will turn on the
5782     embed_files package which then embeds the entire MITgcm source code
5783     (*.[fFhc] + Makefile) used for the build within the executable
5784     - requested by CNH but off by default
5785     - adds a paltry <9MB to the mitgcmuv executable in most cases
5786     - only writes the output when useEMBEDSRC in eedata is true
5787 heimbach 1.597 o clean up 3-dim. relaxation codes:
5788     * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
5789     * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
5790     * Thanks to Tom Haine for testing!
5791    
5792 jmc 1.1203 checkpoint57z_post (2005/12/31)
5793 jmc 1.593 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
5794     affects output (@ truncation level) of exp. plume_on_slope ; updated.
5795 mlosch 1.592 o fix the pickup behavior for obcs in combination with ptracers
5796     o fix a bug in ptracers_external_fields_load
5797     o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
5798     affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
5799     o transfered surface NH pressure to eta field (if exactConserv).
5800 jmc 1.589 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
5801     and update lab_sea output.txt file.
5802 heimbach 1.590 o completing 3-dim. relaxation code: additional term
5803     1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
5804     in S/R EXTERNAL_FORCING_T (file external_forcing.F)
5805     * At compile time, in "EXF_OPTIONS.h" set
5806     #define ALLOW_CLIMTEMP_RELAXATION
5807     #define ALLOW_CLIMSALT_RELAXATION
5808     * At runtime in "data", under &PARM03 set (e.g., units in seconds)
5809     tauThetaClimRelax3Dim = 15552000.0,
5810     tauSaltClimRelax3Dim = 15552000.0,
5811     * 3 cases:
5812     1) Use a constant-in-time 3-dim. field
5813     2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
5814     3) Real-time relax. to time-evolving prescribed field
5815 heimbach 1.595 o Adding Laplacian-type smoothness constraint on
5816     initial and boundary (forcing) controls (ic, bc)
5817     * enable at compile-time via
5818     ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
5819     * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
5820 heimbach 1.594 * Absolute scale somewhat unclear so far
5821     * no area weighting was included since no other cost term does so far
5822 jmc 1.589
5823 jmc 1.1203 checkpoint57y_post (2005/12/08)
5824 heimbach 1.588 First step for a NLFS adjoint
5825     o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
5826     o new init. routines for calc_r_star, calc_surf_dr
5827     o still need to deal with ini_masks_etc
5828     o testreport seemed happy
5829 jmc 1.1203 checkpoint57y_pre (2005/12/08)
5830 heimbach 1.587
5831 jmc 1.586 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
5832 stephd 1.585 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
5833 stephd 1.584 o add new offset feature to offline pkg (plus minor cleanup)
5834     o cfc fixes for final year of integration
5835     o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
5836     be in GCHEM_OPTIONS).
5837    
5838 jmc 1.1203 checkpoint57x_post (2005/12/04)
5839 jmc 1.583 o fix testreport Pb in multiple test experiment.
5840 edhill 1.582 o cleanup our namelist syntax in verification:
5841     - make it more F95 standards compliant (some work still needed)
5842     - allows the vast majority of our tests to work with gfortran
5843 jmc 1.580 o Non-Hydrostatic:
5844     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
5845     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
5846 jmc 1.579 o Allow to apply AB on T,S rather than on AB(gT,gS):
5847     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
5848     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
5849     time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
5850     - need a "clever" read_pickup to restart from the other AB formulation
5851 jmc 1.578 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
5852     o remove some unused variables (reduces number of compiler warnings)
5853 heimbach 1.581 o adjoint
5854     * Disable useVariableViscosity for adjoint for time being
5855     (there are a number of extensive recomputations)
5856     * Initialize certain variables needed for adjoint
5857 jmc 1.578
5858 jmc 1.1203 checkpoint57w_post (2005/11/03)
5859 jmc 1.576 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
5860     fix the singleCpuIO RS version of MDSWRITEFIELD
5861     and add a WARNING if using globalFiles=T with multi-processors.
5862 jmc 1.575 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
5863     using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
5864 jmc 1.576 o tracer advection scheme:
5865 jmc 1.574 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
5866     those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
5867     was not very convenient).
5868     add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
5869     (further tests needed for the implicit DST & Flux-Limiter schemes).
5870 mlosch 1.573 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
5871     and sRef for convenience, handy, when you want to initialize
5872     ptracers in a large domain with a constant non-zero value. Also,
5873     untangle ptracers_init.F a little.
5874    
5875 jmc 1.1203 checkpoint57v_post (2005/10/13)
5876 jmc 1.572 o change dome exp. to use variable viscosity in side-drag terms.
5877 edhill 1.570 o remove all the files from the cfc_offline test since they are now
5878     incorporated into tutorial_cfc_offline which has been producing
5879     identical results for a few days of testing
5880 jmc 1.571 o add new parameter: sideDragFactor to enable half-slip-side BC
5881     and change side-drag S/R to use viscosity from mom_calc_visc
5882     (can switch back by setting sideDragFactor=0.); affects results at
5883     truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
5884     global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
5885 jmc 1.569 o vorticity & strain are now computed without masking, to account for
5886     no-slip-side BC in variable viscosity calculation ; mask is applied
5887     anyway later on, before computing advection/coriolis terms.
5888 mlosch 1.573 o modify exp4 to test new obcs support for reading from external files
5889 mlosch 1.568 and for passive tracers
5890 mlosch 1.567 o fix behavior of ptracers_monitor when monitor output is written to a
5891     netcdf-file; still not independent of monitor.F (writes in the same
5892     file).
5893 jmc 1.566 o change default value of tRef (put a uniform, meaningful value for ocean
5894     & atmos) and initialize sRef (was missing, as Martin mentioned).
5895 baylor 1.565 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
5896     to be proportional to enstrophy dissipation length. Thus,
5897     viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
5898     This is now consistent with Smagorinsky and with the manual.
5899    
5900 mlosch 1.564 checkpoint57u_post
5901 mlosch 1.562 o OBCS and PTRACERS: add open boundary support for passive tracers
5902     - either use homogenous (pseudo) v.Neumann conditions or prescribe
5903     OB-values from file; this is not different from the way theta and salinity
5904     are treated
5905     - however, Orlanski-radiation conditions are not supported, and the model
5906     will stop if you use pTracers and Orlanski at the same time.
5907     - beefed up the rountine obcs_external_fields_load: now only those open
5908     boundary values are overwritten with values from files for which there
5909     are really files, otherwise the OB-fields remain untouched. This makes
5910     it possible to use different OBs at different ends of the domain (as
5911     with EXF)
5912 jmc 1.561 o reduce number of exch calls in shap_filt (s2).
5913 jmc 1.560 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
5914     truncation level) 4/5 MLAdjust test results (11&12 digits match).
5915    
5916 jmc 1.1203 checkpoint57t_post (2005/10/03)
5917 jmc 1.558 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
5918     o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
5919     same truncation, independent of the face number: affects affects several
5920     test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
5921 jmc 1.557 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
5922 jmc 1.558 note that biharmonic viscosity + no-slip was not tested in any experiment.
5923 jmc 1.556 o fix bug in non-linear free-surf side-drag ; generate new output for
5924     global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
5925 edhill 1.555 o make mnc honor the writeBinaryPrec flag for most kinds of output
5926 edhill 1.554 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
5927 jmc 1.553 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
5928     error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
5929 jmc 1.552 o add brackets in multi-terms sum to get same truncation, independent of
5930     the face number (manage to get exactly same value of gU,gV at the cs-edge)
5931     affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
5932 baylor 1.551 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
5933     and viscA4Remax, which allow one to limit the minimum viscosity by specifying
5934     a maximum grid-scale Reynolds number. Also, changes all length calculations
5935     in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
5936     Suggested values of viscosity parameters found in mom_calc_visc.
5937     Many new viscosity diagnostics available.
5938 jmc 1.550
5939 jmc 1.1203 checkpoint57s_post (2005/09/20)
5940 baylor 1.549 o Add clearing-house for viscosity calculations, mom_calc_visc and
5941     correct numerous bugs in LeithD and Smagorinsky discretizations.
5942     mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
5943     used simultaneously, and to be used in mom_vecinv and mom_fluxform.
5944     Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
5945     and with Strain-Tension viscous term calculation (mom_hdissip.F).
5946     The Strain-Tension form is now called with useStrainTensonVisc=.true.
5947     ViscAhStrain and viscAhTension are now retired.
5948 jmc 1.550 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
5949 edhill 1.547 o In response to JMC's bug report, genmake2 now ignores any soft-links
5950     that it finds in the *current* directory when searching for files.
5951     Soft-links found in any other source directories will still work as
5952     they did before.
5953 edhill 1.546 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
5954     a C routine to unlimit the stack size
5955 edhill 1.545 o mnc-ify pkg/aim snapshot vars
5956 edhill 1.544 o mnc-ify pkg/land as requested by Daniel
5957 edhill 1.543 o various changes to mnc including:
5958     - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
5959     - output can now be grouped so that all files within a group
5960     change the ITER portion of their names in lock-step together
5961     - can now read ("global") PER-FACE (in addition to PER-TILE) files
5962     and works with both EXCH1 and EXCH2 (but needs more testing)
5963     - writing works for all verification test cases w/ g77 on Linux
5964    
5965 jmc 1.1203 checkpoint57r_post (2005/09/07)
5966 edhill 1.541 o make MNC variable initialization happen earlier
5967 jmc 1.540 o add diagnostics for (almost) each term of the momentum Eq.
5968 jmc 1.537 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
5969 jmc 1.536 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
5970     o remove MINIMAL_TAVE_OUTPUT option ;
5971     add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
5972 jmc 1.535 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
5973     allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5974 heimbach 1.538 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
5975     o add time-dependent SST, SSS control
5976 heimbach 1.539 o cost terms in ecco/ modularized (new cost_generic.F)
5977     o cost_averages routines are modularized (new cost_averagesgeneric.F)
5978     o new infrastructure for seaice model vs. obs misfits in seaice/
5979     * driver from the_main_loop.F is seaice_cost_driver.F
5980     * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
5981     * gradient check in Exp. 6a of natl_box_adjoint/
5982     o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
5983     (see README file)
5984 jmc 1.535
5985 jmc 1.1203 checkpoint57q_post (2005/08/19)
5986 jmc 1.533 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
5987 edhill 1.531 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
5988     - bug was reported by Jean-Michel and Ian Fenty
5989 jmc 1.532 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
5990     update exp. cpl_aim+ocn output.
5991 heimbach 1.530 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
5992     Needed for high-res. runs with large global files
5993     to be able to limit tapelev size
5994     o Changed some tests for adjoint:
5995     * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
5996     * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
5997     * global_ocean.90x40x15/ back to default 3-level checkpointing
5998 heimbach 1.534 o Modifications to enable scripted COMMON to MODULE conversion
5999     * verification/OpenAD/code/ has necessary scripts and description;
6000     * converts, compiles and runs successfully;
6001 heimbach 1.530
6002 jmc 1.1203 checkpoint57p_post (2005/08/01)
6003 jmc 1.529 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
6004     o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
6005     (already the case for some pkgs, including recent MNC_init, e.g. thsice)
6006     o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
6007 jmc 1.527 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
6008     (was already the case for dissipation with mom_vecinv,
6009     and also the case for grad.PhiHyd when staggered-timeStep)
6010     This will allow to put dissipation out-off the AB time-stepping.
6011     Unfortunately, affects truncation error. Update output of exp. that "fails"
6012     (cg2d matching number) and leave the others for later: front_relax(10),
6013     global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
6014     matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
6015    
6016 jmc 1.1203 checkpoint57o_post (2005/07/30)
6017 edhill 1.525 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
6018     (2) its ready to be documented during the 20050801 DocFest
6019 edhill 1.524 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
6020     for ideal_2D_oce and lab_sea on linux_ia32_g77
6021 heimbach 1.526 o set to #undef CTRL_SET_OLD_MAXCVARS_30
6022     in global1x1_tot/code_seaice_adj to access indices 32, 33
6023     (worth another tag)
6024 edhill 1.524
6025 jmc 1.1203 checkpoint57n_post (2005/07/29)
6026 heimbach 1.521 o adding precip control xx_precip 32
6027     o adding swflux control xx_swflux 33
6028 heimbach 1.522 o Replacing 10 forcing penalty cost routines by 1 generic.
6029     o Implementing partitioning in time-mean and variable adjustment
6030     for atmos. state.
6031     o Time-mean constant error is now read in data.ecco (instead of hard-coded)
6032 heimbach 1.519 o in natl_box_adjoint:
6033 heimbach 1.522 * updated exp 1 to 10
6034     (but does not have time-mean vs. variable split results yet)
6035 heimbach 1.523 o updated global1x1/*_seaice_adj/
6036     to incorporate latest changes
6037 heimbach 1.520 o enable useSingleCpuIO for mdsio vector routines
6038     (applies in particular to tapelev I/O)
6039     o removed inefficient K-loop in all active_file*control*.F
6040 heimbach 1.518
6041 jmc 1.1203 checkpoint57m_post (2005/07/28)
6042 jmc 1.516 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
6043     and advect_cs (use EXCH-2 and standard cs-32 grid files).
6044 jmc 1.515 o pkg/exch2: filling of face-corner halo regions is optional
6045     (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
6046    
6047 jmc 1.1203 checkpoint57l_post (2005/07/14)
6048 jmc 1.514 tag before updating tutorials (pre-release-2)
6049 jmc 1.513 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
6050     for output and interpolation of input fields onto model grid)
6051     o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
6052     Affects results of exp. rotating_tank ; update output.txt.
6053 jmc 1.511 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
6054 jmc 1.512 and taking the square quantity and/or using a fraction-weight field.
6055 jmc 1.511 o fix aim_diagnostics_init.F mate numbers.
6056     o add mnc output capability to diagnostics/diagstat and update
6057 edhill 1.510 our cvsignore files for the ACSII output generated
6058    
6059 jmc 1.1203 checkpoint57k_post (2005/07/02)
6060 heimbach 1.509 o lab_sea now uses diagnostics package and provides a suite of
6061     new EXF diagnostics output.
6062    
6063 jmc 1.1203 checkpoint57j_post (2005/06/30)
6064 heimbach 1.508 o exf
6065     * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
6066     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
6067     terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
6068     * extended diagnostics output
6069     - now includes all EXF variables
6070     - hs, hl moved to common block
6071     - separate S/R for diagnostics, called after ctrl vector is added
6072     - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
6073     - EXFqnet contains true Qnet (i.e. includes qsw)
6074     * updated verif. lab_sea, global_with_exf
6075     * Rearranging hflux (exf_mapfields -> exf_getforcing)
6076     to ensure that diagnostics sees a true EXFqnet
6077 jmc 1.507 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
6078 jmc 1.506 o diagnostics pkg: change pointers so that 1 diagnostic can be used
6079     several times with different frequencies.
6080 edhill 1.505 o mnc-ify the thsice package as requested by Daniel Enderton
6081     - the monitor--MNC output needs work
6082     - many attributes need to be added (most are currently blank)
6083     o mnc-ify theaim_v23 package as requested by Daniel Enderton
6084     - many attributes need to be added (most are currently blank)
6085 jmc 1.503 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
6086 jmc 1.502 o add Sadourny like discretization to the 4th.O vorticity advection scheme
6087 jmc 1.500 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
6088 jmc 1.501 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
6089     fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
6090 jmc 1.499 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
6091     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
6092    
6093 jmc 1.1203 checkpoint57i_post (2005/06/19)
6094 molod 1.497 o Diagnostics package was changed: diagnostic allocation is now deactivated
6095     by setting an empty file name in the namelist (used to be by setting 0 frequency)
6096 jmc 1.496 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
6097     add 1rst Order upwind vertical Shear.
6098 edhill 1.495 o add a quick fix for A/B checkpointing in OFFLINE mode
6099 edhill 1.494 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
6100     end-run around the C/Fortran linking horror in eesup/src/timers.F
6101 adcroft 1.493 o added pkg/runclock: allows user to terminate run based on wall clock
6102     o added non-hydrostatic scaling parameter: nh_am2
6103 mlosch 1.492 o pkg/my82: futile attempt to make results compiler-independent by adding
6104     some "_d 0", etc. no effect.
6105 edhill 1.491 o for mnc output, fill the 'T' coordinate var with myTime and create a
6106     separate 'iter' variable for iteration count
6107 jmc 1.489 o pkg/diagnostics:
6108 jmc 1.490 add new capability: output of Global/Regional & per-level statistics ;
6109     tested against monitor output (including land & thSIce) on various exp.
6110     o make seaice-pkg I/O type flags (MNC/MDS) more standard.
6111 jmc 1.489
6112 jmc 1.1203 checkpoint57h_done (2005/05/19)
6113 jmc 1.488 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
6114     data.diagnostics, data.gchem, data.ptracers) is done.
6115    
6116 jmc 1.487 o pkg/diagnostics: prepare for Global/Regional statistics.
6117     add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
6118 jmc 1.486 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
6119     and rename it: DIFFERENT_MULTIPLE
6120    
6121 jmc 1.1203 checkpoint57h_post (2005/05/14)
6122 jmc 1.485 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
6123 jmc 1.484 o pkg/diagnostics: change output frequency, now in seconds (instead
6124     of Nb of iterations). This requires to change data.diagnostics.
6125 jmc 1.1203 checkpoint57h_pre (2005/05/12)
6126 jmc 1.483
6127 edhill 1.482 o in mnc, let the user create the output dir if both mnc_outdir_date
6128     and mnc_outdir_num are false
6129 edhill 1.481 o add fflags() to pkg/diagnostics which allows one to specify, on a
6130     per-file basis, the file precision [default behavior is unchanged]
6131 dimitri 1.480 o added diagnostics to pkg/kpp, including computation of mixed layer
6132     depth based on a temperature/density criterion
6133     o updated verification/natl_box to test the new pkg/kpp diagnostics
6134 jmc 1.479 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
6135 jmc 1.478 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
6136 edhill 1.477 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
6137     not mnc -- this mistake was found by JMC and is now corrected
6138    
6139 jmc 1.1203 checkpoint57g_post (2005/04/15)
6140 jmc 1.476 o add Adams-Bashforth 3rd Order time stepping:
6141     - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
6142     - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
6143 jmc 1.1203 checkpoint57g_pre (2005/04/15)
6144 jmc 1.475
6145 heimbach 1.472 o make lambda[Theta,Salt]ClimRelax spatially varying
6146     (default remains spatially uniform constant based on tau)
6147 heimbach 1.473 o added new control variables
6148     * init. uVel, vVel, etanN
6149     * lambda[Theta,Salt]ClimRelax
6150     o separate masks used for ctrl_pack/unpack 'from write_grid' output
6151     (suggested by G. Forget)
6152 heimbach 1.472
6153 jmc 1.1203 checkpoint57f_post (2005/04/06)
6154 jmc 1.471 o add parameter "baseTime" = model base time = time at iteration zero
6155     new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
6156     account for baseTime shift
6157     o move Coriolis arrays from PARAMS.h to GRID.h
6158 jmc 1.1203 checkpoint57f_pre (2005/04/06)
6159 jmc 1.470
6160 edhill 1.468 o mnc-ifying the seaice package
6161 adcroft 1.467 o introduced an alternative length scale calculation for use in the limiting
6162     maximum viscosity (off by default, see mom_vi_hdissip.F for details)
6163 heimbach 1.466 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
6164 baylor 1.465 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
6165     as well as grad(vort3). Made it compatible with both approximate form
6166     for the cubed sphere and full form of these gradients. Added flag
6167     useFullLeith to select between approximate and full form.
6168 jmc 1.464 o add "d0" in getcon.F to reduce differences between compilers/platforms
6169     update output.txt of exp. fizhi-gridalt-hs
6170 jmc 1.463 o change port_rand funtion to allow to set the seed.
6171 edhill 1.462 o fix obscure MNC bug involving conversion between reals and integers
6172     - it caused no problems with certain (eg. gcc, ifc) compilers but the
6173     new version is now more standards-compliant
6174 heimbach 1.469 o adjoint-related modifications
6175     * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
6176     * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
6177     * mom_vi_hdissip: to be able to use Leith scheme in adjoint
6178 edhill 1.462
6179 jmc 1.1203 checkpoint57e_post (2005/02/28)
6180 heimbach 1.461 o Adding eddy stress controls a la Ferreira et al.
6181 jmc 1.474 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
6182 heimbach 1.460
6183 jmc 1.459 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
6184     update output.txt of exp. fizhi-gridalt-hs
6185 edhill 1.458 o add more "Z" dimensions and associated coordinate vars to MNC
6186 dimitri 1.457 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
6187 dimitri 1.456 o parameter calendarDumps: when set, approximate months (30-31 days) and years
6188     (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
6189     KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
6190     months and years. Requires pkg/cal.
6191 edhill 1.455 o diagnostics: add pickup functionality
6192     - off by default for backwards compatibility
6193     - current version only uses MDSIO -- MNC will be added
6194 jmc 1.454 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
6195 jmc 1.452 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
6196    
6197 jmc 1.1203 checkpoint57d_post (2005/02/11)
6198 jmc 1.451 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
6199 edhill 1.450 o modify verification/ideal_2D_oce so that it tests the creation of mnc
6200     output from the diagnostics package
6201 jmc 1.449 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
6202 edhill 1.448 o make genmake2 more portable by using ".$FS" instead of ".f" for more
6203     of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
6204 edhill 1.447 o add coordinate variables to the MNC output from the diagnostics package
6205 jmc 1.446 o change MNC-flags default value: true when useMNC=TRUE
6206 edhill 1.444 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
6207     the ability (off by default) to read the grid information using MNC
6208 jmc 1.445 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
6209 jmc 1.443 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
6210 jmc 1.442 o do snap-shot diagnostics at the middle of the time-interval (instead of
6211     at the end).
6212 jmc 1.441 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
6213     new test for AIM with thSIce + slab-ocean
6214 jmc 1.440 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
6215 jmc 1.439 o move state variable diagnostics to the beginning of the time step ;
6216     (note: still needs some work specially for snap-shot diagnostics)
6217     duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
6218    
6219 jmc 1.1203 checkpoint57c_post (2005/01/27)
6220 jmc 1.438 o Change testing option (-ieee) to get closer agreement between g77 & ifort
6221     o generate new output.txt files on faulks with g77 & the new -ieee option
6222 jmc 1.1203 checkpoint57c_pre (2005/01/27)
6223 jmc 1.437
6224     o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
6225 jmc 1.436 update output.txt of exp. global_ocean.90x40x15
6226 jmc 1.435 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
6227     results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
6228 jmc 1.432 o add saltFlux(+File) forcing capability with periodicExternalForcing
6229 jmc 1.431 o allow to use pkg diagnostics for GM-Redi & ThSIce output
6230     o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
6231 edhill 1.430 o improvements for the MNC output from DIAGNOSTICS:
6232     - correct handling of the unlimitied dimension
6233     - all dims now have associated coordinate variables
6234     - variables located at U, V, and Corner ("Z") points are now written
6235     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
6236     *all* data points are output
6237 dimitri 1.429 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
6238 dimitri 1.428 o added pkg/seaice/seaice_monitor.F
6239 dimitri 1.427 o mdsio_readfield.F can now read files visible only to master MPI process.
6240 dimitri 1.426 o pkg/seaice: some test code for ice-modified ocean stress
6241 dimitri 1.425 o exf_getffields interpolation defaults to bilinear for all scalar forcing
6242     fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
6243     spurious negative numbers for precipitation and humidity. Will cause
6244     some small numerical differences for integrations using pkg/exf/exf_interp.F.
6245 heimbach 1.434 o pkg/ctrl/
6246     * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
6247     May be enabled via doPackDiag
6248     * introduce z-scaling of
6249     + gradient (doZscalePack) and
6250     + control (doZscaleUnpack)
6251     o pkg/mdsio/
6252     * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
6253     * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
6254 dimitri 1.425
6255 jmc 1.1203 checkpoint57b_post (2004/12/20)
6256 jmc 1.424 o simplify options in diagnostics_fill arguments (remove weird combinations)
6257 edhill 1.423 o fix MNC coordinate variables so that they now contain per-face index
6258     values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
6259     general, EXCH2 grids are only aligned to a "local" coordinate system
6260 jmc 1.422 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
6261     o Implement instantaneous output within pkg diagnostics:
6262     setting a negative frequency in data.diagnostics produces
6263     "snap-shot" output (as opposed to time-average if freq > 0)
6264 jmc 1.421 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
6265     NOTE: change ptracer diagnostics name: use 2 characters to work with
6266     more than 9 tracers. Add also diagnostics of advect & diffus flux.
6267 edhill 1.420 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
6268     becomes the coordinate variable for the 'T' dimension
6269 edhill 1.419 o add CF-style coordinate variables to MNC
6270     - just a first cut: numbers are meaningless on the cubesphere and
6271     missing along the T axis but otherwise it works!
6272 dimitri 1.418 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
6273 jmc 1.417 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
6274 jmc 1.416 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
6275     this is based directly on what the model compute, so that the content of
6276     each diagnostics might be affected by switching options (e.g., implicitDiffusion)
6277     o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
6278 mlosch 1.415 o clean up build options files for SunOS, in particular
6279     - remove -traditional from xmakedepend
6280     - change -xarch=v9 to -xarch=native for f77
6281     - restore use of make (not gmake)
6282     - add CC=gcc if using g77
6283 edhill 1.413 o changes per discussion of AM, JMC, & EH3 today:
6284     - move redundant "grid" variables out of "state" -- in preparation of
6285     creating proper CF-style coordinate variables and in recognition
6286     that any/all grid variables can be easily copied (eg. w/NCO) from
6287     the grid files into any of the other NetCDF files
6288     - *always* output grid variables with MDSIO (this will eventually be
6289     changed)
6290     - output MNC grid file if useMNC is true
6291 edhill 1.412 o every instance of _END_MASTER() has been found and replaced with
6292     _END_MASTER( myThid ) in order to satisfy certain picky Sun
6293     preprocessors
6294 jmc 1.411 o re-arrange diagnostics pkg initialisation:
6295     - allow each package to extend the available diagnostics list
6296     - add some checking and fix small problems (multi-threaded, ...)
6297     - new S/R diagnostics_fill (replace fill_diagnostics):
6298     look through the short list of active diag. (instead of the long list)
6299     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
6300 edhill 1.381
6301 jmc 1.1203 checkpoint57a_post (2004/12/10)
6302 heimbach 1.410 o this set of changes restores TAMC compatibility
6303     tested for global_ocean.90x40x15 adjoint on trough
6304     (what a pain)
6305    
6306 jmc 1.1203 checkpoint57a_pre (2004/12/10)
6307 heimbach 1.409 o some modifs in tools/build_options for sunos
6308     o call ctrl_pack for ctrl at end for optimcycle=0
6309    
6310 jmc 1.1203 checkpoint57 (2004/12/09)
6311 mlosch 1.406 o add horizontal bi-harmonic viscosity for vertical velocity
6312     - new parameter viscA4W (defaults to viscA4)
6313     - affects only non-hydrostatic code
6314     - to be done: no-slip lateral boundary conditions
6315 dimitri 1.405 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
6316 jmc 1.404 o implement Implicit Vertical advection for pTracers
6317 jmc 1.401 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
6318 jmc 1.402 (implemented also for implicit vertical diffusion & advection)
6319 mlosch 1.400 o OBCS: extend application of tracer open boundary conditions
6320     to a strip beyond the boundary of width Olx/Oly
6321 heimbach 1.403 o add call monitor to TAF set of required calls (flow directives)
6322     and include in natl_box_adjoint
6323     o untangle a few ifdefs related to cost, ctrl, autodiff
6324     untangel a few ALLOW_ECCO_OPTIMIZATION
6325 heimbach 1.407 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
6326     (theta2, salt2 in ecco_cost_weights)
6327 mlosch 1.400
6328 jmc 1.1203 checkpoint56c_post (2004/12/03)
6329 mlosch 1.399 o OBCS as control variables
6330     - update ctrl_ad_diff.list, obcs_ad_diff.list
6331     - remove balance of obcs controls from default
6332     - fix index bug nobcs in ctrl_init
6333     - fix dummy fields filen in ctrl_pack
6334     - add dummy weights for obcs
6335     o lsopt: comment out fort.94 output
6336     o optim:
6337     - remove unnecessary header files
6338     - adjusted namelists
6339     - add xerbla.F to Makefile
6340     o exf:
6341     - multiple modifications of exf_check_range
6342     - unit change in exf_init_runoff from [m/year] to [m/s]
6343     o mdsio:
6344     - i/o-vector change debugLevel from debLevA to debLevB
6345    
6346 jmc 1.1203 checkpoint56b_post (2004/12/01)
6347 mlosch 1.397 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
6348     is called from DO_THE_MODEL_IO
6349     - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
6350     - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
6351     - clean up PTRACERS_WRITE_TIMEAVE a little
6352 mlosch 1.396 o add another verification experiment that tests both the cfc-pkg and
6353     the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
6354     reactive tendencies treated inline with regular timestepping
6355 mlosch 1.395 o testreport previously did a lousy job of comparing small numbers, so
6356     we (Ed and Martin) changed the way the cut-off of 1.e-12 is
6357     implemented in the little c-progam tmp_cmpnum.c which is embedded in
6358     testreport.
6359     o ptracers_monitor: bug fix for MPI
6360    
6361 jmc 1.1203 checkpoint56a_post (2004/11/28)
6362 mlosch 1.394 o GCHEM: finish reorganizating the package
6363     - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
6364     (introduces another 3D-array for each passive tracer, but only if
6365     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
6366     gchemTendency is not needed because the timestep is done separately)
6367     - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
6368     - GCHEM is now---more or less cleanly---separate from PTRACERS
6369     - to bo done: handling of surfaceForcingPtr that is needed for KPP not
6370     so clear to me how that should be done in a general way.
6371     o CFC: improve formatting of output in CFC_ATMOS
6372     o PTRACERS:
6373     - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
6374     that ALL experiments with ptracers enable can be checked. This makes
6375     GCHEM_MONITOR obsolete.
6376     - include a runtime parameter PTRACERS_monitorFreq that defaults to
6377     monitorFreq
6378     - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
6379 edhill 1.393 o add PTRACERS (PTR0[1-5]) to testreport output
6380 heimbach 1.391 o exf_check_range:
6381     * default changed to .TRUE.
6382     * will check values for niter0 if debLevA, every timestep if debLevB
6383     * STOP in exf_check_range if 'out of range'
6384     * range chosen generous to allow for potential extema
6385     TBD: a version with stricter range
6386     permitted range would be runtime parameters
6387 jmc 1.390 o GMredi:
6388     - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
6389     - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
6390     - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
6391 mlosch 1.388 o GCHEM:
6392     - move call to GCHEM_FORCING_SEP, so that it is now called before
6393     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
6394     - introduced a useGCHEM runtime flag and applied it everywhere.
6395 mlosch 1.392 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
6396     this flag is now only visible within GCHEM-pkg routines.
6397     - moved gchem_forcing_int temporarily into ptracers_forcing, this will
6398     be replaced by a 3D array that is computed before thermodynamics; for
6399     this, the tracer ID iTracer had to be included into the parameter list
6400     of ptracers_forcing
6401 mlosch 1.394 - set up forward_step to call gchem_forcing, that will replace
6402 mlosch 1.392 gchem_forcing_int in ptracers_forcing
6403     - cleaning up
6404 jmc 1.389 o small cleaning of exch2: remove files that are also in eesupp/src
6405 mlosch 1.387
6406 jmc 1.1203 checkpoint56 (2004/11/17)
6407 jmc 1.385 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
6408 edhill 1.384 o mnc: cleanup "full" files--fixes out-of-memory problem
6409 heimbach 1.386 o ECCO-GODAE
6410     * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
6411     * fully merged and updated from SIO code
6412     windstress sign change affects
6413     - exf_inscal_[u/v]stress
6414     - sign of xx_tau[u/v] adjustments
6415     - signs in cost_scat
6416     * ctrl_get_gen: avoid update of tau[u/v] for first few days
6417     * natl_box_adjoint updated and compressed
6418     * 2-level checkpoint switch added
6419     (tested in EXP. 1 of natl_box_adjoint)
6420     * new switch doInitXX to avoid init. of xx_... in optimcycle=0
6421     o SVD
6422     * first complete, non-hacked version for SVD calculations
6423     * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
6424     performed via direct access files admtlm_vector.it????
6425     (via ctrl_[un]pack)
6426     * optimcycle is used for ARPACK iteration counter
6427     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
6428     * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
6429     and add linear transforms where necessary
6430     * controls are initial/final SST, SSS (can be extended; need to check
6431     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
6432     o mdsio: filename info to both stderr, stdout
6433     o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
6434     from sign change
6435 edhill 1.384
6436 jmc 1.1203 checkpoint55j_post (2004/11/10)
6437 jmc 1.382 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
6438     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6439 edhill 1.381 o add consistent build directories and .cvsignore files to verification
6440 dimitri 1.380 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
6441 edhill 1.379 o make all subroutines 30 or less characters in length for certain older
6442     compilers to work (a thorough search only turns up two routines in
6443     pkg/ptracers)
6444 jmc 1.378 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
6445     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6446    
6447 jmc 1.1203 checkpoint55i_post (2004/10/28)
6448 jmc 1.376 o change arrays for total vertical diffusivity (2.D if explicit,
6449     3.D if implicit) ; each ptracer uses its own background value.
6450 edhill 1.375 o added mnc/NetCDF output capability to ocn_compon_interf
6451     - added bits to verification/cpl_aim+ocn so that it can run on
6452     ITRDA and other clusters without the mpirun "-wd" option
6453 afe 1.374 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
6454     configuration
6455 edhill 1.373 o give MNC the ability to create additional files rather than
6456     exceeding a specified file size limit "MNC_MAX_FILESIZE"
6457     - the default is just less than 2GB which is a practical limit
6458     on many systems
6459 jmc 1.372 o Compute the non-local term using either KPP vertical diffusivity (=default)
6460     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
6461 jmc 1.349
6462 jmc 1.1203 checkpoint55h_post (2004/10/20)
6463 jmc 1.371 o add verification test "vermix"
6464 edhill 1.370 o remove all the *_ioinc flags and replace with the single global
6465     outputTypesInclusive flag
6466 jmc 1.369 o allow to set a vertical profile of vertical diffusivity for T & S
6467 jmc 1.371 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
6468     o useMNC moved from data.mnc to data.pkg
6469 jmc 1.369
6470 jmc 1.1203 checkpoint55g_post (2004/10/14)
6471 heimbach 1.368 o Renaming carbon AD experiments to comply with testreport conventions
6472     o Updating adjoint of Held-Suarez hs94.1x64x5
6473     o Fixing directives for non-ECCO forward_step, after ECCO directives
6474     have been fixed to avoid recomp. of do_oceanic_phys
6475     Works well for global_ocean.90x40x15,
6476     but recomp. issue remains for carbon
6477     o Updating adjoint output for natl_box_adjoint after
6478     pkg/ecco has been modified (see taga c55d_post)
6479    
6480 jmc 1.1203 checkpoint55f_post (2004/10/13)
6481 edhill 1.367 o rename to timeave_init_fixed
6482    
6483 jmc 1.1203 checkpoint55e_post (2004/10/13)
6484 heimbach 1.366 o some delicate re-shuffle of store directives to avoid one
6485     extra call of do_oceanic_physics
6486     affects ecco_the_main_loop.F, do_oceanic_physics.F
6487     checkpoint_lev1_directives.h
6488     o NB: this may break global_ocean adjoint temporarily,
6489     but it is clear how to fix it. Will do later, need this now.
6490    
6491 jmc 1.1203 checkpoint55d_post (2004/10/11)
6492 heimbach 1.365 o ECCO specific cost function terms (up-to-date with 1x1 runs)
6493     o ecco_cost_weights is modified to 1x1 runs
6494     o modifs to allow observations to be read in as
6495     single file or yearly files
6496     o enable to read exf forcing fields as either
6497     single file or yearly files (flag useExfYearlyFields)
6498 jmc 1.1203 checkpoint55d_pre (2004/10/08)
6499 heimbach 1.365
6500     o switch between 2-level and 3-level checkpointing
6501 edhill 1.364 o add ability of MNC to write local and "partial" (eg. 2D slices where
6502     the full 3D field is never actually stored) arrays to NetCDF files
6503     with the correct (that is, the complete multi-dimensional) set of
6504     array indicies
6505     - used in mom_vecinv() to write the diagFreq output
6506     - tested (demonstrated) in verification/aim.5l_cs
6507 edhill 1.363 o further mnc-ification
6508     - add verification/lab_sea to the list with mnc setups
6509     - fix undefined mnc v-names in cd_code
6510     - add kpp to mnc output (both snapshot and timeave)
6511 mlosch 1.362 o non-hydrostatic code
6512     - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
6513     in calc_gw.F
6514     - defaults to viscAh
6515     - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
6516     friction or Leith) in non-hydrostatic mode, as long as there is
6517     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
6518 heimbach 1.360 o pkg/cost
6519     extend simple cost functions to treat time mean quantities
6520     (T,U,V) via cost_accumulate_state from cost_tile
6521 jmc 1.358 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
6522     be 2 times larger than the minimum size the advection scheme requires.
6523     now get a perfect conservation of salt in advect_cs test-exp (updated)
6524 mlosch 1.356 o GGL90 (Gaspar's TKE mixed layer)
6525     - add horizontal diffusion of TKE, requires exchanges in
6526     do_fields_blocking_exchanges, horizontal diffusivity is zero by
6527     default. In OPA there is no horizontal diffusion of TKE but the
6528     mixing coefficients are computed from a horizontal average of TKE of
6529     6 points or so. I think that diffusion has a little more physical
6530     justification.
6531     - clean up ggl90_calc in the hope of reducing memory usage (this hope
6532     was in vain)
6533     - mask tke-variable in ggl90_init
6534 jmc 1.355 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
6535     o fix biharmonic diffusion on CS-grid.
6536 mlosch 1.354 o more obcs stuff
6537     - added obcs_external_fields_load as an alternative to the EXF-pkg option
6538     for reading boundary values. This routine is called from
6539     obcs_prescribe_read
6540     - updated obcs_check
6541 mlosch 1.357 - changed sponge layer relaxation parameter units for days to seconds
6542     - turned off sponge layer by default
6543 heimbach 1.359 - changed argument list of OBCS_CALC to myTime+deltaTclock
6544 mlosch 1.361 - fixed about 35 bugs in obcs_external_fields_load
6545 mlosch 1.354
6546 jmc 1.1203 checkpoint55c_post (2004/09/23)
6547 heimbach 1.352 o obcs stuff
6548     - new runtime flags useOBCSprescribe, useOBCSbalance
6549     - re-arranged obcs_calc
6550     - moved exf_getobcs to obcs_prescibe_read
6551     obcs_prescibe_read is called after ORLANSKI stuff
6552     and independent of it (executable can contain all).
6553     - updated obcs_check
6554 heimbach 1.353 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
6555     These may be necessary only if tangential velocities are
6556     prescribed at OB, not sure, needs testing.
6557 edhill 1.351 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
6558     which simplifies the calls and passes the ifc check-bounds test
6559    
6560 jmc 1.1203 checkpoint55b_post (2004/09/22)
6561 jmc 1.350 o add a 2D scalar, Z location, exchange_2 routine.
6562 jmc 1.349 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
6563     to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
6564     affects advect_cs results (for the wrong reason): update output.txt
6565 jmc 1.348 o use a more standard discretization for biharmonic viscosity ;
6566     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
6567     affects results of dome set-up: update output.txt
6568     o fix gad_advection.F (CubedSphere part), back to version 1.23
6569     o fix bug in mom_vi_del2uv.F (CubedSphere part).
6570 mlosch 1.341
6571 jmc 1.1203 checkpoint55a_post (2004/09/20)
6572 heimbach 1.347 o merged code to
6573     * prescribe/read time-dependent open boundaries
6574     (works in conjunction with exf, cal)
6575     * sponge layer code for open boundaries
6576     * each boundary N/S/E/W now has its own CPP option
6577     (healthy for the adjoint)
6578    
6579 jmc 1.1203 checkpoint55 (2004/09/17)
6580 heimbach 1.346 o up-to-date adjoint of previous breaks
6581     - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
6582     - global_ocean_ebm: adjoint still needs fix (TLM ok)
6583     - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
6584     - carbon: * remove tr1-related adjoint verification
6585     * add ptracer as control variable
6586     o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
6587     (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
6588    
6589 jmc 1.1203 checkpoint54f_post (2004/09/16)
6590 heimbach 1.345 o in verification/carbin/ remove experiment related to
6591     ALLOW_PASSIVE_TRACER (array tr1 etc)
6592     code_ad/ input_ad/ results_ad
6593    
6594 mlosch 1.344 o add two new packages
6595     - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
6596     + subject to optimization (memory)
6597     - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
6598     + subject to reordering (many GOTOs in the original code)
6599     + so far opps is called for every (i,j) point, and then operates in
6600     the vertical; one may want to reorder the scheme in order operate in
6601     horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
6602     fields)
6603 edhill 1.343 o overhaul of IO so that we now have flags for MDSIO and/or MNC
6604     - all verification tests compile and run with linux_ia32_g77
6605     - defaults are compatible with current input files--nothing
6606     should change if you were not previously using MNC
6607     - MNC output has been added in numerous places (eg. timeave)
6608     but there are still a few writes not yet do-able with MNC
6609     (this is in progress)
6610     - flags now allow for either/or/both use of MDSIO and MNC and
6611     documentation will soon follow
6612     - numerous small formatting cleanups for ProTeX
6613 edhill 1.342 o add version info (via BUILD_INFO.h) to MNC and stdout
6614    
6615 jmc 1.1203 checkpoint54e_post (2004/09/02)
6616 mlosch 1.341 o add two new packages
6617     - pp81 (Packanowski and Philander, 1981), Richardson number and
6618     stratification dependent mixing
6619     - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
6620     - these scheme operate in a similar manner as KPP (without ghat, of
6621     course), however there is only one diffusivity that is used for both
6622 mlosch 1.1068 temperature and salinity (and passive tracers)
6623 stephd 1.340 o add offline package
6624 edhill 1.339 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
6625     provided by Stephanie Dutkiewicz
6626 edhill 1.338 o genmake2: add ability to search for C compilers and cleanup test output
6627     - fixes recent SX-6 problems and should help with others (eg. HP-UX)
6628    
6629 jmc 1.1203 checkpoint54d_post (2004/07/27)
6630 adcroft 1.336 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
6631 jmc 1.337 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
6632     leading to additional shift by 5 days each year of integration
6633     (i.e. leading to considerable offset over the years)
6634 jmc 1.335 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
6635     o start with no AB and no initial filtering (staggerTimeStep):
6636     change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
6637     o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
6638     (external loading & cpl import/export stay in forward_step.F)
6639     o update coupling interface to work with new staggerTimeStep
6640     o change MDSIO ptracers_pickup.
6641 jmc 1.334 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
6642 edhill 1.333 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
6643 jmc 1.334 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
6644 edhill 1.333
6645 jmc 1.1203 checkpoint54c_post (2004/07/18)
6646 jmc 1.331 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
6647     this affects (truncation error) output.txt of test-exp:
6648     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
6649     o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
6650 jmc 1.330 o change Qnet to always be the net heat flux, (+upward).
6651     affects (truncation error) output of natl_box exp.: updated
6652 jmc 1.329 o define the max number of passive tracers in PTRACERS_SIZE.h
6653     o start to test mnc routinely in exp0
6654     o add sea-ice loading (sIceLoad) as a new forcing field.
6655    
6656 jmc 1.1203 checkpoint54b_post (2004/07/08)
6657 edhill 1.327 o add testreport "-j JOBS" option for parallel builds (tested and pretty
6658     impressive on Altix and Opteron systems)
6659 edhill 1.326 o diagnostics can now write NetCDF files through the mnc package
6660 jmc 1.325 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
6661 jmc 1.324 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
6662 jmc 1.323 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
6663     affects (truncation error) output of lab_sea & natl_box exp.: updated
6664     o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
6665    
6666 jmc 1.1203 checkpoint54a_post (2004/07/06)
6667 jmc 1.322 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
6668     o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
6669     o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
6670     o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
6671     + internal_wave (shift in writing cg2d_ini_res)
6672 jmc 1.1203 checkpoint54a_pre (2004/07/05)
6673 jmc 1.321
6674 dimitri 1.320 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
6675     - modified verification/lab_sea and natl_box_adjoint accordingly
6676    
6677 jmc 1.1203 checkpoint54 (2004/07/02)
6678     checkpoint53g_post (2004/07/02)
6679 jmc 1.317 o prepare splitting of thermodynamics: store convect.counter in common block
6680 jmc 1.316 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
6681     output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
6682 dimitri 1.315 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
6683 jmc 1.314 o new parameter "nShapS": allow to treat differently S from T (nShapT)
6684     o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
6685 heimbach 1.318 o restore adjointability
6686 jmc 1.314
6687 jmc 1.1203 checkpoint53f_post (2004/06/25)
6688 jmc 1.313 o modifications that affect AIM experiment results (update output.txt):
6689     - no advection of S at top interface Nr (pkg/generic_advdiff)
6690     - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
6691 jmc 1.312 o AIM pkg:
6692     - include stability function into surf.Flux derivative relative to Tsurf
6693     - calculate clear-sky radiation & surface temp. change (for diagnostics)
6694 jmc 1.313
6695 afe 1.311 checkpoint53e_post
6696     o merged cylindrical coord configuration
6697     o added rotating_tank experiment
6698 afe 1.310 checkpoint53e_pre
6699    
6700 jmc 1.1203 checkpoint53d_post (2004/06/14)
6701 jmc 1.308 o faulks upgraded: re-generate output.txt that have changed:
6702     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
6703 adcroft 1.307 o Added Bryan and Lewis, 1979, vertical diffusivity profile
6704 jmc 1.306 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
6705 adcroft 1.305 o added Sadourny discretization of Coriolis
6706     - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
6707     - re-enabled use of omega3 (useAbsVorticity)
6708 adcroft 1.304 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
6709 jmc 1.309 vector-invariant equations
6710 adcroft 1.304 - note: does *NOT* yet use same variable visc. for no-slip BC's.
6711 mlosch 1.303 o recoded the lateral boundary conditions for non-hydrostatic w, this time
6712     hopefully without new bugs
6713     - still to do: biharmonic friction for non-hydrostatic w
6714 adcroft 1.302 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
6715     o regenerated output for global_ocean_ebm (using -ieee)
6716 adcroft 1.301 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
6717     of mom_common/
6718     - simple re-arrangement of instructions within computing loop
6719 jmc 1.1203 checkpoint53d_pre (2004/05/21)
6720 mlosch 1.297
6721 jmc 1.1203 checkpoint53c_post (2004/05/21)
6722 jmc 1.299 o new version of coupler for AIM+thSIce and Ocean models
6723     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
6724     - land: change Evaporation of snow
6725     - aim with thSIce: fix bug in snow-precip.
6726 mlosch 1.297 o changes to calc_gw.F
6727     - bug fix for w^2 term near the bottom boundary
6728     - (hopefully) improve the lateral slip boundary condtions for use with
6729     partial/looped cells
6730     - because the bug fix changes two verification experiments anyway (exp5
6731     and plume on slope), change the lateral boundary condition from half slip
6732     to the value of no_slip_sides
6733 heimbach 1.298 o ebm package wasnt quite up to the parallel task. Fixed that.
6734 heimbach 1.300 o Adjoint of EBM package + verification
6735     * TLM OK
6736     * ADM not sufficient accuracy yet (needs further testing)
6737 heimbach 1.295
6738 jmc 1.1203 checkpoint53b_post (2004/05/14)
6739 heimbach 1.296 o Commiting new energy balance model to repository
6740     * package is pkg/ebm
6741     * verif. is verification/global_ocean_ebm
6742     * references are in ebm_driver.F
6743     C * X. Wang, P. Stone and J. Marotzke, 1999:
6744     C Global thermohaline circulation. Part I:
6745     C Sensitivity to atmospheric moisture transport.
6746     C J. Climate 12(1), 71-82
6747     C * X. Wang, P. Stone and J. Marotzke, 1999:
6748     C Global thermohaline circulation. Part II:
6749     C Sensitivity with interactive transport.
6750     C J. Climate 12(1), 83-91
6751     C * M. Nakamura, P. Stone and J. Marotzke, 1994:
6752     C Destabilization of the thermohaline circulation
6753     C by atmospheric eddy transports.
6754     C J. Climate 7(12), 1870-1882
6755     o Will need long integration testing.
6756 jmc 1.1203 checkpoint53b_pre (2004/05/14)
6757 dimitri 1.292
6758 adcroft 1.294 o created pkg/mom_common in preparation for variable viscosity code
6759     o renamed and split ini_mnc_io
6760 jmc 1.293 o pkg/land: only liquid water can diffuse or run-off
6761     o AIM using land: soil wetness availability account for snow
6762 dimitri 1.292 o added printMapIncludesZeros to EEPARMS namelist
6763 heimbach 1.290
6764 jmc 1.1203 checkpoint53a_post (2004/05/11)
6765 heimbach 1.290 o restore TAMC compatiility for exf_constants.h
6766     (no usage of _d in .h)
6767     o Additional storing in KPP in an attempt to fix
6768     TAMC problem with adjoint of KPP code.
6769     (no success...)
6770     Identical code works fine with TAF.
6771 dimitri 1.291 o Fixed verification/natl_box_adjoint experiments.
6772     Initial conditions for Experiments 4 and 5 are now
6773     set to "SEAICE_initialHEFF=0", which is more reasonable,
6774     and hence gives results closer to that of Experiment 2.
6775     Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
6776 cnh 1.289
6777 jmc 1.1203 checkpoint53 (2004/05/06)
6778 cnh 1.289 o stable checkpoint with up to date adjoint
6779     TLM tests only run for 1st grdchk at the moment. Its unclear if
6780     this is a code problem or a problem with resetting code for g_
6781     variables that is being autogenerated wrong.
6782     Otherwise:
6783     o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
6784     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
6785     are both still in chaos following their security messes.
6786 jmc 1.279
6787 jmc 1.1203 checkpoint52n_post (2004/05/06)
6788 edhill 1.288 o various build (mostly genmake2) changes including:
6789     - ability to build/run more easily within Cygwin and MacOS X
6790     - more complicated Makefiles with a stronger dependence on Gnu Make
6791 dimitri 1.285 o pkg/seaice modifications
6792 dimitri 1.287 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
6793     of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
6794     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
6795 dimitri 1.285 - changed proxy for geostrophic velocity and updated
6796 dimitri 1.286 verification/lab_sea/results/* accordingly
6797 dimitri 1.285 - removed ADI dynamic solver from pkg/seaice
6798     - replaced all occurrences of 1/CSTICE or 1/CSUICE
6799     they caused a segmentation fault under certain circumstances
6800 mlosch 1.283 - removed unused field WATR
6801 mlosch 1.282 o bug fix in exf-package:
6802     - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
6803     now reflect that.
6804 mlosch 1.281 o small fixes in the cal-package:
6805     - set reference date to first of January for the 'model'-calendar
6806     - failing of cal_CheckDate in cal_FullDate now actually results in a
6807     warning
6808 mlosch 1.280 o small modifications in exf-package to increase flexibility:
6809     - change climtempfreeze from a constant to a runtime parameter that
6810     is specified in data.exf_clim (default = -1.9)
6811     - introduce runtime parameter windstressmax (default = 2.0) that is
6812     specified in data.exf
6813 jmc 1.279 o fix in pkg/thsice:
6814     - update Evap (Tsf changes) to be consistent with Latent heat flux
6815     - maintain snow precipitation unchanged (even if Tsf >=0).
6816     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
6817 edhill 1.272
6818 jmc 1.1203 checkpoint52m_post (2004/04/18)
6819 mlosch 1.277 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
6820     this does not change any of the results, because myIter=0 in swfrac always
6821     lead to jwtype=2 (the default anyway), but the call makes little sense
6822     as a default
6823 jmc 1.276 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
6824 jmc 1.275 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
6825     atmospheric model (AIM) to use it ; add a "slab ocean" component.
6826     o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
6827     o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
6828 dimitri 1.274 o extending useSingleCpuIO option to work with new exch2 I/O format
6829     - old-style, missing-tile I/O is still accessible by defining CPP
6830     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
6831 edhill 1.273 o monitor package can write to NetCDF files and/or STDOUT
6832     o fix re-definition bug in MNC_GRID_INIT_ALL()
6833 edhill 1.272 o doc/api_reference added
6834     - a framework for building an API Reference Manual using all
6835     the "protex" comments embedded in the code
6836     - see pkg/generic_advdiff, pkg/mnc for examples
6837 edhill 1.269 o MNC:
6838     - make myThid the last argument for all subroutines
6839     - new default for the grid files: NO halos
6840 edhill 1.270 - add useMNC and other run-time flags
6841     - separate per-file-group handling of the unlimited dimension
6842     - early initialization of MNC w/ flags read at the eeboot stage
6843     and lookup tables set in initialize_fixed
6844     - write all MNC output to a freshly-created directory
6845 jmc 1.268 o thermodynamics sea-ice (thsice) is now tested with testreport.
6846     o test exp. advect_cs: use the standard cs32 grid ; update output.
6847 heimbach 1.271 o Added functionality to grdchk:
6848     pick global i,j,k position (or nearest wet) where to perform check.
6849 jmc 1.266
6850 jmc 1.1203 checkpoint52l_post (2004/03/11)
6851 jmc 1.267 o new land formulation:
6852     a) use ground enthalpy as prognostic variable to ensure exact
6853     energy conservation.
6854     b) account for water temperature and for latent heat of freezing
6855     in all processes (rain, run-off, ground storage)
6856     c) compute surface and ground temperature implicitly.
6857     o aim_v23 modification for new land model:
6858     a) Treat separately land / ocean / sea-ice surface fluxes
6859     to allow implicit computation of land & sea-ice surface temp.
6860     b) add snow precipitation.
6861 jmc 1.1203 checkpoint52l_pre (2004/03/11)
6862 jmc 1.266
6863 jmc 1.265 o fix problem (when 1 tile is empty) in min/max monitor.
6864     o fix bug in timeAve (u,vZetatave in common block)
6865 dimitri 1.264 o no restoring terms under ice for pkg/seaice
6866 dimitri 1.263 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
6867     o bug fix for pkg/seaice pickups
6868 edhill 1.262 o change MNC call locations and add coordinate attributes
6869 jmc 1.260 o mask vorticity at the corner ; affects global_ocean.cs output
6870     o fix ini_curvilinear_grid ; test CS experiments with mpi
6871 jmc 1.259 o aim.5l_cs: modify sea-ice fraction input file ; update output
6872 heimbach 1.261 o exf: Adding simple range check routine for exf fields after read
6873 adcroft 1.256
6874 jmc 1.1203 checkpoint52k_post (2004/02/23)
6875 adcroft 1.256 o removed top-level directory "diags"
6876     - we migrated these functions to pkg/timeave a long time ago
6877     o fixed bug introduced in pkg/monitor
6878 heimbach 1.257 o accuracy ctrlprec = 32 insuffient for gradient checks using
6879     averaged fields (I/O via cost_averages)
6880     -> use ctrl.h in active_file*.F to control I/O precision.
6881     o paramter list of CALL ADTHE_MAIN_LOOP
6882     o added initial do_the_model_io to ecco
6883     o set all ...Freq to zero after cost_final
6884     taveFreq, dumpFreq, pChkptFreq
6885 heimbach 1.258 o MAIN and ECCO differentiability restored
6886 heimbach 1.255
6887 jmc 1.1203 checkpoint52j_post (2004/02/18)
6888 heimbach 1.255 o fix nchklev in tamc.h for global_ocean...
6889     o Bringing flow and store directives up-to-date
6890     o Really weird thing!
6891     call do_the_model_io from the_main_loop with parameters
6892     starttime, niter0, instead of mytime, myiter, screws up the adjoint:
6893     TAF places a faulty re-call of initialise_varia
6894     after cost_final call which should not be there!
6895 jmc 1.1203 checkpoint52j_pre (2004/02/03)
6896 jmc 1.253
6897 afe 1.254 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
6898     error messages
6899 jmc 1.253 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
6900 afe 1.252 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
6901     debug output
6902 afe 1.251 o modfied mdsio_writefield.F to handle non-global files under exch2
6903 jmc 1.250 o update AIM Cubed-Sphere exp (aim.5l_cs):
6904     use land, p*, and Franco.M forcing fields with fractional land-sea mask.
6905     o update AIM Equatorial Channel exp:
6906     use standard aim_v23 pkg and change the SST fields to be more realistic.
6907 afe 1.248 o globalFile now works with exch2
6908 afe 1.247 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
6909 jmc 1.253 mon_vort3.F to make exch2 friendly with >1 tile per cube face
6910 dimitri 1.249 o limit timeave output for hi-res integrations
6911 adcroft 1.245
6912 jmc 1.1203 checkpoint52i_post (2004/01/21)
6913 adcroft 1.245 o removed CPP_EEOPTIONS.h from verification/*/code
6914     o updated the tiling for global_ocean_pressure
6915 jmc 1.1203 checkpoint52i_pre (2004/01/20)
6916 jmc 1.246
6917     o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
6918     the old pkg/aim).
6919 afe 1.239
6920 jmc 1.1203 checkpoint52h_pre (2004/01/20)
6921 afe 1.243 o shortened offending lines in exch2_send_rx?.template
6922 afe 1.242 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
6923 edhill 1.240 o genmake2: add build & execute test for NetCDF code
6924 afe 1.239 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
6925     old grid files, moved CPP_EEMACROS.h to pkg/exch2
6926 dimitri 1.238 o added useSingleCPUIO flag to monitor.F and mon_out.F
6927 dimitri 1.241 o added temporary hack for sea-ice dynamics on the cube:
6928     metric terms are ignored and it is assumed that
6929     there is no sea-ice on cube faces 1, 2, 4, and 5.
6930 dimitri 1.238
6931 jmc 1.1203 checkpoint52f_post (2004/01/09)
6932 afe 1.236 o added exch2 cube routines to pkg/exch2
6933     o modified hs94.cs-32x32x5 to use it
6934     o added new grid files to hs94.cs-32x32x5
6935 jmc 1.1203 checkpoint52f_pre (2004/01/07)
6936 dimitri 1.228
6937 jmc 1.1203 checkpoint52e_post (2004/01/07)
6938 jmc 1.234 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
6939     for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
6940 jmc 1.235 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
6941     to work with implicit vertical advection and AB ;
6942     o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
6943     o update output (gad_calc_rhs.F changes affect truncation error) of exp:
6944     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
6945 jmc 1.1203 checkpoint52e_pre (2004/01/02)
6946 jmc 1.233
6947     o fix bug in impldiff when Nr=1 or Nr=2.
6948 jmc 1.232 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
6949     o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
6950 jmc 1.229 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
6951     ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
6952 dimitri 1.228 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
6953 dimitri 1.231 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
6954     o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
6955 jmc 1.220
6956 jmc 1.1203 checkpoint52d_post (2003/12/16)
6957 adcroft 1.230 o re-tiled many expts to allow comparison in multi-processor mode
6958     - updated output accordingly
6959     - changed hs94.128x64x5 to use intial T from file rather than use the
6960     random number generator
6961 molod 1.227 o add infrastructure in model routines for fizhi and gridalt packages
6962 jmc 1.220 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
6963 dimitri 1.222 o changes to permit hi-res, cubed-sphere, configuration
6964     - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
6965     - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
6966     - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
6967     of surface winds for the cube
6968     (A verification experiment, based on global_ocean.cs32x15, but with
6969     pkg/seaice turned on and with on-the-fly interpolation from the NCEP
6970     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
6971     complete with example surface forcing files and matlab scripts to look
6972     at the output and compare it with that of global_ocean.cs32x15.)
6973 jmc 1.223 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
6974     but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
6975     to conform to the common rule.
6976 jmc 1.224 o check-in the first version of the coupler + interfaces for multi-components
6977     set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
6978     - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
6979     - atmosphere: use pkg aim_v23 ; no sea-ice for now.
6980     - ocean and atmos. share the same horizontal grid (no interpolation).
6981     - exchanges between component and coupler is done in forward_step
6982 jmc 1.225 o new verification experiment, cpl_aim+ocn:
6983     coupled ocean - AIM atmosphere on cs32 grid.
6984 jmc 1.217
6985 jmc 1.1203 checkpoint52d_pre (2003/12/06)
6986 jmc 1.217 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
6987 jmc 1.218 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
6988 heimbach 1.213
6989 jmc 1.1203 checkpoint52c_post (2003/11/25)
6990 heimbach 1.213 o Fixing OPTIONS files for use of exf:
6991     - ALLOW_ECCO not needed
6992     - ECCO_CPPOPTIONS.h should not be included from
6993     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
6994     as has been the case in the past
6995     - All cal/exf related options are currently set in
6996     single header file. Should remain so until we
6997     agree on a consistent new policy.
6998 heimbach 1.214 o Removed all CPP options for cal package.
6999     cal has no more CPP options.
7000 heimbach 1.215 o modified STOREs in GAD_ADVECTION
7001     o corrected key comp. for passkey
7002 heimbach 1.210
7003 jmc 1.1203 checkpoint52b_post (2003/11/23)
7004 jmc 1.212 o new version: "thsice" of thermodynamic sea-ice pkg:
7005     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
7006     - modify fluxes but do not change theta directly;
7007     - light cleaning of bulk_force pkg (still needed with thsice).
7008     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
7009     + output_thsice.txt to test thsice & bulk_force pkgs.
7010     o put back grid & coriolis monitor output.
7011 jmc 1.1203 checkpoint52b_pre (2003/11/23)
7012 jmc 1.211
7013     o call "do_the_model_io" at the beginning (=> dump initial state)
7014     o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
7015 heimbach 1.210 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
7016     (need info on NUMBER_OF_PTRACERS)
7017     o missing PTRACERS headers in some routines
7018     o default tamc.h in pkg/autodiff supposed to crash
7019     to ensure proper customization
7020 dimitri 1.206
7021 jmc 1.1203 checkpoint52a_post (2003/11/17)
7022 jmc 1.208 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
7023 dimitri 1.207 - moved surfaceTendencyTice from pkg/seaice to main code
7024 jmc 1.208 - subroutine FREEZE_SURFACE now limits only surface temperature
7025     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
7026     => new output.txt for global_ocean.cs32x15 & global_with_exf
7027     - keep the old version of FREEZE for backward compatibility;
7028     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
7029 heimbach 1.209 - corresponding modifs for TAF directives
7030 dimitri 1.207 o added surface flux output variables to TIMEAVE_STATVARS
7031     o time-averaged output for pkg/ptracers
7032 heimbach 1.209 o fix problem with ECCO-related divided adjoint
7033     snapshot file was missing some ad-variables,
7034     but no warning issued by TAF
7035 dimitri 1.206
7036 jmc 1.1203 checkpoint52a_pre (2003/11/12)
7037 dimitri 1.206 o some bug fixes for #undef REAL4_IS_SLOW
7038 heimbach 1.205
7039     checkpoint52 = ecco_c52_e35
7040     o after testing adjoints of checkpoint51u_post
7041 edhill 1.203
7042 jmc 1.1203 checkpoint51u_post (2003/11/06)
7043 heimbach 1.204 o this is the post-merge tag of the ecco-branch
7044     (needs another clean checkout and re-testing)
7045     o various natl_box_adjoint configs and results
7046     but no input fields
7047     o obcs adjoint not yet merged!
7048     o adding ECCO global 1x1 and 2x2 degree configs
7049     o updated/extended some store directives for seaice
7050     o pkg/ecco now containes ecco-specific part of cost function
7051     o top level routines the_main_loop, forward_step
7052     supersede those in model/src/
7053     previous input data.cost now in data.ecco
7054     (new namelist ecco_cost_nml)
7055     o in ctrl/ cleaned some cross-dependencies and updated CPP options
7056    
7057 jmc 1.1203 checkpoint51t_post (2003/11/04)
7058 heimbach 1.204 o this is the pre-merge tag of the ecco-branch
7059    
7060 jmc 1.1203 checkpoint51s_post (2003/11/04)
7061 edhill 1.203 o cleanup: removed various obsolete #define-s
7062 heimbach 1.204 o pkg/grdchk
7063     - renamed 'ph-grd 3' to 'grad-res'
7064     - merged from ecco-branch
7065     (remaining bug fixes for obcs gradient checks)
7066     - additional high-precision output for testreport
7067     (grep for 'precision_grdchk_result')
7068 edhill 1.202
7069 jmc 1.1203 checkpoint51r_post (2003/11/03)
7070 edhill 1.202 o cleaned up or removed CPP_OPTIONS.h files
7071     o updated results for some of the tests to reflect the new
7072     optfiles (-ieee: -O0 instead of -O3)
7073 heimbach 1.201
7074 jmc 1.1203 checkpoint51q_post (2003/10/30)
7075 heimbach 1.201 o cd_code:
7076     - moved cd_scheme.F -> cd_code_scheme.F
7077     - separate read_checkpoint from cd_code_ini_vars.F
7078     - separated cd_code part from write_checkpoint
7079     - updated AD_SOURCE, generated .flow
7080     - added CD_CODE_VARS.h to the_main_loop
7081     - Moving cd_code specific store dir.s to pkg/cd_code
7082     o ctrl package totally restructured
7083     - pack/unpack now optional and decoupled from
7084     xx_/adxx_ I/O
7085     - ctrl_pack/unpack cleaned
7086     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
7087     - confined inclusion of AD_CONFIG.h to where necessary.
7088     o genmake2: changed AD dependencies from SRCFILES to AD_FILES
7089 edhill 1.198
7090 jmc 1.1203 checkpoint51p_post (2003/10/30)
7091 edhill 1.198 o create initial cd_code package
7092 edhill 1.199 - WARNING: the initialization of fields within packages
7093     is broken because INI_FIELDS (where READ_CHECKPOINT is
7094     called) is called *before* PACKAGES_INIT_VARIABLES.
7095     This seems to be backwards since
7096     1) its important to initially zero the entire field including
7097     the "halo" region
7098     2) zeroing needs to be done *before* reading pickup info
7099     and the pickup call might or might not happen in any
7100     particular run
7101     - this needs an overhaul for R2
7102 edhill 1.198 o cleanup verification/*/code/GMREDI_OPTIONS.h
7103     o cleanup testreport
7104 heimbach 1.196
7105 jmc 1.1203 checkpoint51o_post (2003/10/27)
7106 heimbach 1.196 o bringing AD-related verif's up to date with genmake2
7107     - carbon/
7108     - global_ocean.90x40x15/
7109     - hs.94.1x64x5/
7110     - (front_relax/ )
7111     o (more) consistent directory structure for AD-related verif.'s
7112     o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
7113     o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
7114     o bug fix in find_alpha.F for MDJWF:
7115     - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
7116     change rho -> rho-rhoConst
7117     - replace call find_rho to find_rhonum
7118     o initialisation of rFlx extended to full array (required by TAF)
7119     and shifted to thermodynamics
7120     o removed PTRACERS.h in ptracers routine
7121     o added surfacetendencyPtr to S/R parameter list pracers_forcing
7122     o Correcting initialisations for fVerU, fVerV.
7123     o helping TAF to recognize dependency on kUp for
7124     fVerU, fVerV
7125     o Replacing delZ by delR in pkg/ctrl/
7126 jmc 1.1203 checkpoint51o_pre (2003/10/24)
7127 dimitri 1.192
7128 edhill 1.195 o undid all of cp51 pending some cleanups and discussion
7129 heimbach 1.197 o added the [#include "AD_CONFIG.h"] statement to all files that need
7130     it for adjoint/tl #defines
7131     o re-worked the build logic in genmake2 to support AD_CONFIG.h
7132     o removed tools/genmake since it no longer works
7133 dimitri 1.194
7134 jmc 1.1203 checkpoint51n_post (2003/10/23)
7135 dimitri 1.194 o modifications to make FREEZE flux visible to pkg/kpp
7136     - moved surfaceTendencyTice from pkg/seaice to main code
7137     - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
7138     - subroutine FREEZE now limits only surface temperature
7139     (this means new output.txt for global_ocean.90x40x15,
7140     global_ocean.cs32x15, and global_with_exf)
7141     o added surface flux output variables to TIMEAVE_STATVARS
7142    
7143 jmc 1.1203 checkpoint51n_pre (2003/10/23)
7144 dimitri 1.192 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
7145 edhill 1.193 o added [#include "AD_CONFIG.h"] to all files that use the following
7146     defines:
7147     - ALLOW_ADJOINT_RUN
7148     - ALLOW_TANGENTLINEAR_RUN
7149     - ALLOW_ECCO_OPTIMIZATION
7150 edhill 1.190
7151 jmc 1.1203 checkpoint51m_post (2003/10/21)
7152 edhill 1.190 o incorporating changes to get TAMC/TAF working in genmake2
7153     - added new TAMC/TAF targets to the Makefile
7154     - various cleanups related to package handling
7155 edhill 1.191 - these changes should have no impact on the forward model
7156 dimitri 1.189
7157 jmc 1.1203 checkpoint51l_post (2003/10/20)
7158 dimitri 1.189 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
7159     - faster algorithm for cal_addtime.F
7160     - higher precision arithmetic, where needed
7161     - pkg/exf *startdate variables changed from calendar date to
7162     model integration time
7163    
7164 jmc 1.1203 checkpoint51l_pre (2003/10/17)
7165 jmc 1.188 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
7166     o enable to apply restoring on S & T only in a latitude band.
7167     o update output (external_forcing_surf modif. change truncation errors)
7168     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
7169 edhill 1.186
7170 jmc 1.1203 checkpoint51k_post (2003/10/16)
7171 jmc 1.187 o change default to: useNHMTerms=.FALSE.
7172     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
7173     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
7174     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
7175     exp1, ideal_2D_oce
7176     - change data file of oceanic exp (leave the results unchanged for now)
7177     exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
7178     o set gravitySign automatically according to the vertical coordinate used
7179     (and change sign: back to "logical" value: +1 when R increases downward)
7180 edhill 1.186 o added an include barrier to the default CPP_OPTIONS.h and
7181     removed the #include "PACKAGES_CONFIG.h" from it
7182 jmc 1.187 o fix a bug in mom_fluxform (from chk51j_post)
7183 heimbach 1.185
7184 jmc 1.1203 checkpoint51j_post (2003/10/10)
7185 heimbach 1.185 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
7186     o adjusted some flow directives (dynamics, thermodynamics)
7187     o added cubed-sphere case to test cost function
7188     o heckpoint_lev?_directives.h now include
7189     pkg-specific directives, whenever those are enabled.
7190     o Moving pkg-specific flow directives to corresponding pkg
7191     Moving pkg-specific differentiation list to corresponding pkg
7192     Moving pkg-specific checkpoint-lev storing to corresponding pkg
7193     ---> conventions are
7194     - pkg_ad.flow
7195     - pkg_ad_diff.list
7196     - pkg_ad_check_lev?_dir.h
7197 stephd 1.181
7198 jmc 1.1203 checkpoint51i_post (2003/10/09)
7199 edhill 1.184 o merge of the branch-genmake2
7200     - knowingly breaks the older genmake
7201     - automatic generation of all ALLOW_${PKG_NAME} defines
7202     - new testreport supersedes older testscript
7203     o large number of package inclusion and header cleanups
7204 jmc 1.1203 checkpoint51i_pre (2003/10/08)
7205 edhill 1.184
7206 edhill 1.183 o new output for adjoin of global ocean vector invariant
7207     o fix for checkpoint of thermodynamic seaice and bulk_force
7208     o Steph gchem various cleanups
7209    
7210 stephd 1.181 checkpoint 51h_pre
7211 edhill 1.183 o fixed some single quotes
7212 stephd 1.181 o modify gchem pkg to be more versatile
7213     o modifications to clean up dic pkg
7214     o add pkg/cfc
7215 heimbach 1.182
7216 jmc 1.1203 checkpoint51g_post (2003/10/02)
7217 heimbach 1.182 o provide links for ARPACK and ADM*TLM
7218     o start removing verification/vero/
7219     o update AD-related stuff
7220     (in particular some IF-statements in model/src/ routines)
7221     o adding to verification/global_ocean.90x40x15/ adjoint of
7222     vector invariant setup
7223 dimitri 1.177
7224 jmc 1.1203 checkpoint51f_post (2003/10/02)
7225 jmc 1.179 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
7226 dimitri 1.178 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
7227 dimitri 1.177 of tracer Green's fucntions for ocean inversion project.
7228 dimitri 1.175
7229 jmc 1.1203 checkpoint51f_pre (2003/08/07)
7230 dimitri 1.175 o Added on-the-fly spatial interpolation capability
7231     "USE_EXF_INTERPOLATION" to pkg/exf.
7232 dimitri 1.176 - This is a temporary Cartesian-grid hack until
7233 dimitri 1.175 the super-duper ESMF coupler becomes available.
7234 dimitri 1.176 - See verification/global_with_exf/README for usage example.
7235     - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
7236     flags and modified pkg/seaice accordingly.
7237 dimitri 1.175 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
7238     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
7239     non-local transport term.
7240 heimbach 1.172
7241 jmc 1.1203 checkpoint51e_post (2003/08/03)
7242 jmc 1.174 o pkg/mom_vecinv:
7243     - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
7244     - add time-ave diagnostic of vorticity advection.
7245     o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
7246     o atmospheric geopotential: - include water vapor effect;
7247     - use p^kappa in p* scaling.
7248 jmc 1.173 o land pkg: read initial state from files.
7249     o AIM : add stratospheric drag in the upper level
7250    
7251 jmc 1.1203 checkpoint51d_post (2003/07/18)
7252 jmc 1.173 o change function ILNBLNK (=> last non-blank char.) to return zero
7253     (instead of the string length) when the string. char is empty
7254 jmc 1.171 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
7255 heimbach 1.172 o modif's to restore TAMC compatibility
7256     - avoid "_d" constructs in PARAMETER declarations
7257     - avoid interrupting lines by comment lines
7258     o Use cluster local disks for purely local I/O
7259     vs. globally visible disks needed for ctrl stuff
7260     (merged from ecco-branch)
7261     - new active_file_loc... and mdsio_..._loc routines
7262     - affected packages: autodiff, ctrl, grdchk, mdsio
7263 heimbach 1.169
7264 jmc 1.1203 checkpoint51c_post (2003/07/08)
7265 heimbach 1.170 o introducing integer flag debugLevel
7266     - debLevZero: suppress all output
7267     - debLevA: standard
7268     - debLevB: equivalent to current debugMode=.TRUE.
7269     o introducing pathname variable mdsioLocalDir for mdsio
7270     that can be specified at runtime
7271     (relevant for cluster I/O to local disk)
7272     `
7273 heimbach 1.169 >>>checkpoint51b_post
7274     adjoint of ptracers
7275     o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
7276     o extended state in checkpoint_lev?, etc.
7277     o alternative ctrl/cost with tr1 or ptracer
7278     o new comlev1_bibj_ptracers
7279     o new ptracers.flow
7280     o made ptracers_forcing same as external_forcing_s
7281     o added verification for adjoint with ptracers
7282     - adm. grdchk fail so far
7283     - tlm. grdchk OK
7284     - checked tapelev/comlev recomputations: OK
7285     <<<checkpoint51b_pre
7286 stephd 1.168
7287 jmc 1.1203 checkpoint51a_post (2003/06/25)
7288 stephd 1.168 o added code for biogeochemistry package
7289     - new pkgs: dic, gchem
7290     - new subroutine in ptracers
7291     o modify code for biogeo packages
7292     - in model/src and pkg/ptracers
7293 heimbach 1.166
7294 jmc 1.1203 checkpoint51 (2003/06/24)
7295 heimbach 1.166 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
7296     - autodiff, ctrl, exf, grdchk, seaice
7297     kept separate packages
7298     - cost, ecco, obcs
7299 heimbach 1.167 o updating verification/internal_wave, verification/lab_sea
7300     (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
7301 heimbach 1.165
7302 jmc 1.1203 checkpoint50i_post (2003/06/23)
7303 heimbach 1.165 o Preparing next differentiable checkpoint and sync
7304     of MAIN vs. ecco-branch
7305     - 1st step: this one is differentiable
7306     - 2nd step: next(! not this) checkpoint will have updated packages
7307     from ecco-branch)
7308 jmc 1.161
7309 jmc 1.1203 checkpoint50h_post (2003/06/20)
7310 jmc 1.163 o new package "land": provide surface BC for AIM.
7311     o pkg/ptracers: apply exchange to all tracers after reading a pickup.
7312 jmc 1.161 o AIM: use true log-P extrapolation for near surface temp (= as in
7313     F.Molteni paper) ; update aim.5l_cs output.
7314 adcroft 1.162 o New variable in PARM03 for more flexible pickups
7315 heimbach 1.164 o somewhat cleaned package initialisation sequence for
7316     ctrl/ cost/ ecco/ in packages_... routines
7317 dimitri 1.160
7318 jmc 1.1203 checkpoint50g_post (2003/05/23)
7319 dimitri 1.160 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
7320     - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
7321     - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
7322     made the default because of faster convergence than ADI
7323 heimbach 1.159
7324 jmc 1.1203 checkpoint50f_post (2003/05/23)
7325 heimbach 1.159 o exf totally restructured
7326     - replaced all exf_set_ routines by one generic exf_set_gen.F
7327     and made sure it's still differentiable
7328     - split exf_getffields.F into new exf_bulkformulae.F
7329     - exf_inscal_/exf_outscal_ suffixes consistent with field names
7330     - updated adjoint/makefile and relevant verif. accordingly
7331 adcroft 1.156
7332 jmc 1.1203 checkpoint50f_pre (2003/05/23)
7333 jmc 1.157 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
7334     + change Evap over land. (update aim.5l_cs output)
7335 adcroft 1.156 o added missing .cvsignores and made uniform across expts
7336     o changed configuration of tidal_basin_2d expt
7337     o added pkg/debug functions for tracing code in fatal crashes
7338     o tidied pkg/monitor to use MONITOR_OPTIONS.h
7339     o new fn in pkg/monitor to stop model if solution grows too big
7340     o removed lots of single quotes from comments
7341    
7342 jmc 1.1203 checkpoint50e_post (2003/05/14)
7343 mlosch 1.155 o make KPP work with PTRACERS
7344     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
7345     nearly a copy of kpp_transport_s
7346     - there is no analogue to SurfaceTendencyS, so I have to use
7347     gPtr(of the surface layer) instead
7348     o add a new platform SunFire+mpi (SunFire 15000) to genmake
7349 jmc 1.1203 checkpoint50e_pre (2003/05/13)
7350 mlosch 1.155
7351 jmc 1.1203 checkpoint50d_post (2003/05/13)
7352 mlosch 1.154 o change kpp output from multiple-record state files to single-record state
7353     files analogous to write_state.F
7354     o reduce the output frequency of cg3d-related stuff to the monitor frequency,
7355     analogous to the cg2d-related output.
7356 mlosch 1.155 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
7357     so that writing to internal file fn (with length 512) fails.
7358 jmc 1.1203 checkpoint50d_pre (2003/05/12)
7359 jmc 1.151
7360 jmc 1.1203 checkpoint50c_post (2003/05/12)
7361 jmc 1.153 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
7362 jmc 1.152 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
7363 jmc 1.151 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
7364     o bug fixed in convective adjustment diagnostic (multi-tile set-up).
7365     o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
7366 dimitri 1.150
7367 jmc 1.1203 checkpoint50c_pre (2003/04/30)
7368 dimitri 1.150 Merging from release1_p13:
7369     o bug fix for pkg/seaice dynamic solver
7370     o Added SEAICE_initialHEFF to pkg/seaice
7371 jmc 1.149
7372 jmc 1.1203 checkpoint50b_post (2003/04/17)
7373 jmc 1.149 o store u*,v* in gU,V instead of in guNm1,gvNm1
7374     o in order to put the momForcing out of the Adams-Bashforth:
7375     move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
7376     to timestep.F
7377     o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
7378     o re-generate output for highly sensitive test-exp:
7379     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
7380 heimbach 1.146
7381 jmc 1.1203 checkpoint50b_pre (2003/04/17)
7382 jmc 1.147 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
7383 heimbach 1.146 o corrected CPP option mismatch in exf_Bulk... functions for case
7384     #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
7385 heimbach 1.145
7386 jmc 1.1203 checkpoint50a_post (2003/03/21)
7387 heimbach 1.145 o Bug fix for merging between c50 and KPP.
7388     ikey was passed from thermodynamics to kpp_calc via
7389     common block rather than being recomputed in kpp_calc,
7390     in contradiction with new key itdkey.
7391     New key ikppkey created, and tamc.h headers updated.
7392 heimbach 1.143
7393 jmc 1.1203 checkpoint50 (2003/03/08)
7394 heimbach 1.144 - 2nd step of merge with ecco-branch:
7395     merge changes in ecco-branch back into main trunk
7396     - bug fix in find_alpha
7397     - more storing in gmredi_calc_tensor.F, kpp_routines.F
7398     - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
7399     - merged some sliced AD support routines
7400    
7401 jmc 1.1203 checkpoint49 (2003/03/06)
7402 heimbach 1.143 merged from ecco-branch:
7403     o exf:
7404     - Enable initialisation of forcing fields to constant
7405     (runtime) values.
7406     - in exf_getffields.F
7407     Reduce i-/j-loop to interior domain, discarding overlaps.
7408     That also fixes wrong TAF-key computations for key_1, key_2
7409     with bulf formulae.
7410     - exf_init.F modify #ifdef for exf_init_evap
7411     - exf_getffieldrec.F, ctrl_getrec.F
7412     The following INT-usages are not safe:
7413     fldsecs = int(fldsecs/fldperiod)*fldperiod
7414     fldcount = int(fldsecs/fldperiod) + 1
7415     and were modified.
7416     o autodiff: checkpoint_lev...
7417     - updated storing for bulk formulae (some arrays were missing)
7418     - added state for seaice package
7419     - synchronized with main branch
7420     o DIVA:
7421     Modif.s in
7422 heimbach 1.144 - the_main_loop.F
7423     - the_model_main.F
7424 heimbach 1.143 and added cost_final_restore.F cost_final_store.F
7425     o With these changes, it is possible to fully separate
7426     the first forward run to compute the cost function (mdthe_main_loop)
7427     and adjoint runs over individual DIVA intervals (adthe_main_loop)
7428     into separate model executions.
7429     This enables better tuning of DIVA to given queue sizes.
7430     o Loss of cost function value in consecutive DIVA runs is
7431     fixed by storing to 'costfinal' file.
7432     o Appropriate call of ctrl_unpack/_pack,grdchk_main at
7433     beginning/end of adjoint integration is accounted for.
7434     The current changes apply to TAF-1.4.26.
7435     TAF has one remaining bug, requiring one manual change
7436     (see MITgcm manual).
7437     o cal: synchronized between MAIN and ecco-branch
7438 heimbach 1.141
7439 jmc 1.1203 checkpoint48i_post (2003/03/05)
7440 heimbach 1.141 o Changes to restore differentiability of code w.r.t. previous tag
7441     (mostly adding new routines to make list and replacing
7442     pressure by totPhiHyd).
7443     o Updated and merged grdchk package
7444     - has both ADM and TLM checks
7445     - works for single- and multi-proc.
7446     - output cleaned
7447     - worked successfully for parallel DIVA
7448     o genmake:
7449     - Adding -platform=SP4
7450     - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
7451     o Modif. for DIVA:
7452     ctrl_unpack should not be called in intermediate DIVA interval.
7453     (similar thing would apply for active files such as
7454     tbar, sbar, psbar, which should not be reinitialised;
7455     only relevant for ecco-branch)
7456 dimitri 1.136
7457 jmc 1.1203 checkpoint48h_post (2003/02/28)
7458 jmc 1.137 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
7459 dimitri 1.136 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
7460     o Added SEAICE_initialHEFF to pkg/seaice
7461 dimitri 1.139 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
7462 jmc 1.135
7463 jmc 1.1203 checkpoint48g_post (2003/02/18)
7464 jmc 1.135 --- EOS:
7465     o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
7466     store total Potential in totPhyHyd for diagnostics & EOS.
7467     o fix restart and overlap Pb when using Z-coord and EOS funct. of P
7468     --- Pressure/geopotential gradient:
7469     o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
7470     o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
7471     ( changes results of global_ocean_pressure )
7472     o NLFS + z-coord.: add eta*Rho' contribution.
7473     o accurate phiHyd when using interface-W at the middle between 2 centers
7474     ( changes results of ideal_2D_oce )
7475     o includes r* 2nd term in potential gradient.
7476 dimitri 1.134
7477 jmc 1.1203 checkpoint48f_post (2003/02/18)
7478 dimitri 1.134 Merging from release1_p12:
7479     o Modifications for using pkg/exf with pkg/seaice
7480     - improved description of the various forcing configurations
7481     - added basic radiation bulk formulae to pkg/exf
7482     - units/sign fix for evap computation in exf_getffields.F
7483     - updated verification/global_with_exf/results/output.txt
7484     o Added pkg/sbo for computing IERS Special Bureau for the Oceans
7485     (SBO) core products, including oceanic mass, center-of-mass,
7486     angular, and bottom pressure (see pkg/sbo/README.sbo).
7487     o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
7488     to avoid negative values in shallow regions.
7489     - updated verification/natl_box/results/output.txt
7490     - updated verification/lab_sea/results/output.txt
7491     o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
7492     o Added useSingleCpuIO option (see PARAMS.h).
7493     o Updated useSingleCpuIO option in mdsio_writefield.F to
7494     work with multi-field files, e.g., for single-file pickup.
7495     o pkg/seaice:
7496     - bug fix in growth.F: QNET for no shortwave case
7497     - added HeffFile for specifying initial sea-ice thickness
7498     - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
7499     o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
7500     kpp_transport_t.F, forward_step.F, and the_main_loop.F
7501     o pkg/seaice:
7502     - adjoint-friendly modifications
7503     - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
7504 jmc 1.131
7505 jmc 1.1203 checkpoint48e_post (2003/02/12)
7506 jmc 1.131 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
7507 jmc 1.132 o dynamics: change definition of computational domain & adapt mom_fluxform
7508     accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
7509     o following exp works with Olx=Oly=2 (and pass through checkbounds option):
7510     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
7511 jmc 1.133 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
7512 jmc 1.132 global_ocean.90x40x15 global_with_exf global_ocean_pressure
7513     inverted_barometer solid-body.cs-32x32x1
7514     (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
7515 jmc 1.130
7516 jmc 1.1203 checkpoint48d_post (2003/02/09)
7517 jmc 1.130 o in preparation for r*:
7518     a) use pre-computed gradient of hydrostatic potential:
7519     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
7520     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
7521     => affects results of glob_oce_pressure (different truncation error)
7522     update output.txt of ideal_2D_oce & global_ocean_pressure
7523 jmc 1.129
7524 jmc 1.1203 checkpoint48d_pre (2003/02/08)
7525 jmc 1.129 o in preparation for r*:
7526     new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
7527     pass the 2 comp. of the grad. as arguments to momentum S/R.
7528     but for the moment, only used if it does not change the results.
7529     o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
7530 jmc 1.126
7531 jmc 1.1203 checkpoint48c_post (2003/02/06)
7532 heimbach 1.128 Modifications in treatment of initial flux forcing controls
7533     to avoid extra storing of flux fields.
7534    
7535 jmc 1.1203 checkpoint48c_pre (2003/01/21)
7536 adcroft 1.127 o Added tidal_basin_2d experiment (currently 1D!)
7537 jmc 1.126 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
7538 jmc 1.124
7539 jmc 1.1203 checkpoint48b_post (2003/01/27)
7540 jmc 1.124 o r* coordinate added in #ifdef NONLIN_FRSURF block.
7541     (modification to pressure gradient not yet implemented)
7542     o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
7543     (for U & V) that are used for vertical advection of momentum.
7544 jmc 1.123
7545 jmc 1.1203 checkpoint48a_post (2003/01/24)
7546 jmc 1.123 o In preparation for r*, use temp. array to compute vertical transport
7547     in flux-form momentum pkg. => change results of few test-exp.
7548     Update output of: exp4, exp5, front_relax, global_ocean_pressure,
7549     lab_sea, natl_box & plume_on_slope
7550 jmc 1.122
7551 jmc 1.1203 checkpoint48 (2003/01/23)
7552 jmc 1.122 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
7553 heimbach 1.121
7554 jmc 1.1203 checkpoint47j_post (2003/01/21)
7555 jmc 1.120 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
7556 heimbach 1.121 o moved adexch from forward_step to addummy_in_stepping
7557     o added exch in ctrl_map_...
7558     o aveFreq.=0. at end of cost_final to avoid overwrite in
7559     reverse checkpointing loop
7560     o Yet more changes in gmredi:
7561     * adgmredi_calc_tensor
7562     avoiding all recomputation of gmredi_slope_limit
7563     * adgmredi_x/y/rtransport
7564     added flag for excessive storing to avoid recomp. of
7565     u/v/rtans, dTdx/y/z
7566     -> this is not really necessary and very memory-consuming
7567     * adgmredi_slope_psi:
7568     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
7569     * gmredi_slope_limit
7570     re-activated full calculation of taperfct for case 'ac02'
7571     o updating verification/ adjoints of carbon, global_ocean.90x40x15
7572 heimbach 1.116
7573 jmc 1.1203 checkpoint47i_post (2003/01/13)
7574 jmc 1.119 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
7575     o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
7576     default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
7577     o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
7578     o gmredi: fix few bugs.
7579    
7580 adcroft 1.118 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
7581 heimbach 1.116 This will be a good checkpoint to plug into the ecco-branch.
7582     o few modif.'s to get latest version adjointed
7583     (mainly kick out code in ini_linear_phisurf)
7584     o modif's to run adjoint with exactConserv
7585     o case GM_BOLUS_ADVEC should be cleaned
7586     S/R gmredi_slope_psi should be cleaned
7587     o verification/carbon now has exactConserv=.TRUE.
7588 jmc 1.114
7589 jmc 1.1203 checkpoint47g_post (2003/01/10)
7590 jmc 1.114 o time-average AIM output: becomes independent from statvars time-average
7591     (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
7592 heimbach 1.115 o After TAF bug fix:
7593     Tested adjoint of gmredi package.
7594     Tests were done with checkpoint47 rather than with latest
7595     checkpoint47f_post since the latter is broken for the adjoint
7596     verification/carbon/ contains both ADM and TLM gradient checks.
7597     Here they are, before they get changed/lost/stolen.
7598     Mostly modif.'s to fix numerical sensitivities.
7599     Gradient checks OK for
7600     - GM_taper_scheme:
7601     * clipping
7602     * ac02
7603     * linear
7604     * glw91
7605     * dm95
7606     * ldd97
7607     - GMREDI_OPTIONS:
7608     * GM_VISBECK_VARIABLE_K
7609     * GM_NON_UNITY_DIAGONAL
7610     * GM_EXTRA_DIAGONAL
7611     * GM_BOLUS_ADVEC
7612     in conjunction with data.gmredi parameters to be checked in
7613     in a few minutes under verification/carbon/code/
7614 cheisey 1.112
7615 jmc 1.1203 checkpoint47f_post (2002/12/28)
7616 dimitri 1.113 Merging from release1_p10:
7617     o modifications for using pkg/exf with pkg/seaice
7618     - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
7619     and SEAICE_EXTERNAL_FLUXES
7620     - pkg/exf CPP options EXF_READ_EVAP and
7621     EXF_NO_BULK_COMPUTATIONS
7622     - usage examples are Experiments 8 and 9 in
7623     verification/lab_sea/README
7624     - verification/lab_sea default experiment now uses
7625     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
7626    
7627 jmc 1.1203 checkpoint47e_post (2002/12/27)
7628 cheisey 1.112 o created a tag prior to creating a branch
7629    
7630 jmc 1.1203 checkpoint47d_post (2002/12/16)
7631 mlosch 1.111 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
7632     at the bottom boundary had an erroneous half slip boundary condition
7633     o added bottom drag and no slip boundary condition capabilities to
7634     oceanic pressure coordinates code
7635     o added new verification experiment global_ocean_pressure, this experiment is
7636     also described in the tutorial section of the manual
7637 jmc 1.1203 checkpoint47d_pre (2002/12/16)
7638 cheisey 1.110
7639 jmc 1.1203 checkpoint47c_post (2002/12/16)
7640 cheisey 1.110 o Added a verification experiment for a global cubed-sphere ocean run
7641     - verification/global_ocean.cubed32x32x30
7642     - uses pkg/therm_seaice and pkg/bulk_forcing
7643 jmc 1.109
7644     o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
7645     o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
7646     when using P-coordinate; only implemented for atmospheric config.
7647     o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
7648     NOTES: requires option NONLIN_FRSURF to be "#define".
7649     o update advect_xz/results/output.txt (left from checkpoint44g_post)
7650 dimitri 1.108
7651 jmc 1.1203 checkpoint47b_post (2002/12/05)
7652 dimitri 1.108 Merging from release1_p9:
7653     o pkg/seaice
7654     - removed GOTO's and added taf directives
7655     - double precision constants to reduce the g77 (Linux)
7656     to F77 (SGI) differences reported in release1_p8
7657     o tools/genmake
7658     - added SGI options
7659     o verification/testscript
7660     - updated to that of checkpoint47a_post
7661     o verification/global_ocean.90x40x15/input/eedata
7662     - modified for SGI f77 compatibility
7663     o verification/lab_sea
7664     - added description of sea-ice model
7665     - added missing matlab routines
7666     - added test of thermodynamics parallelization
7667 jmc 1.105
7668 jmc 1.1203 checkpoint47a_post (2002/11/23)
7669 jmc 1.105 o new pkg: aim_v23
7670     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
7671     for now, keep the same surface forcing as before.
7672     - Part-Cell implemented into AIM; check that Heat & Water are conserved
7673     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
7674     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
7675     o add diagnostic of surface correction term in monitor output
7676 jmc 1.106
7677     o bulk_force and therm_seaice
7678 cheisey 1.107 - Two packages: bulk_force (Bulk forcing)
7679     and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
7680     - Earlier integration from Stephaine Dutkiewicz
7681     and Patrick Heimbach.
7682     - Two ifdef statements for compile time,
7683     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
7684 heimbach 1.104
7685 jmc 1.1203 checkpoint47 (2002/11/15)
7686 heimbach 1.104 differentiable version of checkpoint46n_post
7687     o bug fix in quasihydrostaticterms
7688     o * "clean" adjoint code (in terms of extensive recomputations)
7689     can now be obtained for all GMREDI options (i.e. for
7690     - GM_VISBECK_VARIABLE_K
7691     - GM_NON_UNITY_DIAGONAL
7692     - GM_EXTRA_DIAGONAL
7693     - GM_BOLUS_ADVEC )
7694     * However, wrong gradient check problem remains unsolved.
7695     * New CPP options have been introduced for different
7696     tapering schemes
7697     o external_fields_load now part of differentiation list
7698     o pressure needs multiple storing;
7699     would be nice to have store_pressure at beginning or
7700     end of forward_step, e.g. by having phiHyd global (5-dim.)
7701     (NB: pressure is needed for certain cases in find_rho,
7702     which is also invoked through convective_adjustment).
7703     o recomputations in find_rho for cases
7704     'JMD95'/'UNESCO' or 'MDJWF' are OK.
7705     o #define ATMOSPHERIC_LOADING should be differentiable
7706     o ini_forcing shifted to begining of initialise_varia
7707     o Incorporating QNVS line search routines into MITgcm
7708     (this is separate code, and therefore not under pkg)
7709     lsopt/, optim/
7710     o Updated verification/carbon/
7711     - #define GM_VISBECK_VARIABLE_K
7712     - GM_taper_scheme = 'ldd97'
7713 heimbach 1.103
7714 jmc 1.1203 checkpoint46n_post (2002/11/12)
7715 heimbach 1.103 Merging from release1_p8:
7716     o verification/natl_box:
7717     updating new external_fields_load routine
7718     o New package: pkg/seaice
7719     Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
7720     The sea-ice code is based on Hibler (1979-1980).
7721     Two sea-ice dynamic solvers, ADI and LSR, are included.
7722     In addition to computing prognostic sea-ice variables and diagnosing
7723     the forcing/external data fields that drive the ocean model,
7724     SEAICE_MODEL also sets theta to the freezing point under sea-ice.
7725     The implied surface heat flux is then stored in variable
7726     surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
7727     kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
7728     non-local transport term. Because this call precedes model
7729     thermodynamics, temperature under sea-ice may not be "exactly" at
7730     the freezing point by the time theta is dumped or time-averaged.
7731     N.B.: fairly large differences in accuracy occur across
7732     different platforms/compilers; comparison between
7733     g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
7734     generated output gives:
7735     T S U V
7736     C D M c m s m s m s m s
7737     n p a R g m m e . m m e . m m e . m m e .
7738     f n k u 2 i a a d i a a d i a a d i a a d
7739     g d e n d n x n . n x n . n x n . n x n .
7740    
7741     Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
7742     o GAD:
7743     - generated new common blocks to account for call of
7744     same gad routines with differing traceridentities
7745     (needed to modify tracerIdentity indices in GAD.h)
7746     - generated separate common blocks for case useCubedSphereExchange
7747     (Department of Futurology)
7748     - parameter lists to gmredi_?transport: added tracerIdentity
7749     - added new key indices to tamc.h
7750     o external_fields_load:
7751     - added this routine to TAF list
7752     - needed to make some common blocks global and additional storing
7753     along the same lines as exf package (checkpoint_lev?_directives.h)
7754     o exf:
7755     updated external forcing package
7756     - bug fixes carried over from ecco-branch
7757     (missing OBCS_OPTIONS.h in two routines)
7758     - enable easy to use "no forcing".
7759     - added exf I/O for atmospheric loading
7760     - added exf I/O for runoff data
7761     - transfered scaling between exf <-> MITgcm to exf namelist
7762     o Adding new verification experiment global_with_exf.
7763     This verification experiment is almost identical to the
7764     global_ocean.90x40x15 experiment, except that it uses
7765     the exf (and cal) package instead of the
7766     external_fields_load routine (cf README file).
7767 adcroft 1.94
7768 jmc 1.1203 checkpoint46m_post (2002/11/07)
7769 adcroft 1.101 o modified testscript to return -- when there are no lines of "%MON" output
7770 adcroft 1.100 o added new flag "quasiHydrostatic" for QH mode
7771     and new routine quasihydrostaticterms()
7772 adcroft 1.99 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
7773     New routine: mom_u_coriolis_nh()
7774 adcroft 1.98 o fixed sign of non-hydrostatic metric terms in u and v equations.
7775     Depend on correct sign of gravitySign.
7776 adcroft 1.97 o added work.pc* to .cvsignore in aim directories using ifc
7777 adcroft 1.96 o introduced flag for controllin non-hydrostatic metric terms
7778 adcroft 1.95 o removed gravitySign from PARM04
7779 adcroft 1.94 o switched to g77/ifc from pgf77 in aim experiments
7780 mlosch 1.93
7781 jmc 1.1203 checkpoint46l_post (2002/11/01)
7782 mlosch 1.93 o made convective adjustment work with pressure coordinates:
7783     - changed the direction of k-loop in convective_adjustment.F for the
7784     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
7785     - adjusted the reference pressure k-index in convective_adjustment.F
7786     - adjusted the convection condition in convect.F (in analogy to
7787     calc_ivdc.F)
7788     - convective_adjustment no longer computes anything on the halos
7789     - removed the warnings about negative salinity from find_rho.F and
7790     find_alpha.F; instead the new routine look_for_neg_salinity, called
7791     at the beginning of find_rho, find_alpha, and find_beta, does a
7792     check of the entire slice, if CPP-option
7793     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
7794 jmc 1.1203 checkpoint46l_pre (2002/10/23)
7795 mlosch 1.91
7796 jmc 1.1203 checkpoint46k_post (2002/10/23)
7797 mlosch 1.91 o fixed the verification/global_ocean.90x40x15 experiment:
7798     - new bathymetry (the world according to A., JMC, and M.)
7799     - new initial fields and forcing fields (*.bin files)
7800     - new POLY3.COEFFS (for the next release one should switch to a full
7801     equation of state: JMD95P or MDJWF)
7802     - fixed several errors and redundancies in the data file
7803     - experiment uses looped cells
7804     - added matlab directory with diagnostic scripts for plotting of output
7805 jmc 1.90
7806     o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
7807     - read AIM physics parameters from a file (data.aimphys)
7808     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
7809 jmc 1.89
7810 jmc 1.1203 checkpoint46j_post (2002/10/07)
7811 jmc 1.89 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
7812     o move wVel computation at the end of the time step, in S/R integr_continuity
7813     o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
7814     o update timeave pkg for wVel diagnostic.
7815 jmc 1.1203 checkpoint46j_pre (2002/09/27)
7816 mlosch 1.87
7817 jmc 1.1203 checkpoint46i_post (2002/09/25)
7818 jmc 1.88 o Clean up AIM package (and keep the results unchanged):
7819     include CPP_OPTION and use IMPLICT NONE in all routines ;
7820     declare all the variables _RL ; use _d 0 for all numerical constants.
7821     use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
7822 mlosch 1.87
7823 jmc 1.1203 checkpoint46h_post (2002/09/25)
7824 mlosch 1.87 o cleaned up the use of rhoNil and rhoConst.
7825     - rhoNil should only appear in the LINEAR equation of state, everywhere
7826     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
7827     and the dynamical equations are all divided by rhoConst
7828     o introduced new parameter rhoConstFresh, a reference density of fresh
7829     water, to remove the fresh water flux's dependence on rhoNil. The default
7830     value is 999.8 kg/m^3
7831     o cleanup up external_forcing.F and external_forcing_surf.F
7832     - can now be used by both OCEANIC and OCEANICP
7833 jmc 1.1203 checkpoint46h_pre (2002/09/18)
7834 mlosch 1.87
7835     Added code to convert surface volume flux (fresh water) into
7836     a mass flux when using P coordinates in the ocean (OCEANICP).
7837     Note: It assumes you have set rho0=rhoConst=density of fresh water.
7838 mlosch 1.86
7839 jmc 1.1203 checkpoint46g_post (2002/09/18)
7840 mlosch 1.86 o Include a new diagnostic variable phiHydLow for the ocean model
7841     - in z-coordinates, it is the bottom pressure anomaly
7842     - in p-coordinates, it is the sea surface elevation
7843     - in both cases, these variable have global drift, reflecting the mass
7844     drift in z-coordinates and the volume drift in p-coordinates
7845     - included time averaging for phiHydLow, be aware of the drift!
7846     o depth-dependent computation of Bo_surf for pressure coordinates
7847     in the ocean (buoyancyRelation='OCEANICP')
7848     - requires a new routine (FIND_RHO_SCALAR) to compute density with only
7849     Theta, Salinity, and Pressure in the parameter list. This routine is
7850     presently contained in find_rho.F. This routine does not give the
7851     correct density for 'POLY3', which would be a z-dependent reference
7852     density.
7853     o cleaned up find_rho
7854     - removed obsolete 'eqn' from the parameter list.
7855     o added two new verification experiments: gop and goz
7856     (4x4 degree global ocean, 15 layers in pressure and height coordinates)
7857 jmc 1.1203 checkpoint46g_pre (2002/09/16)
7858 heimbach 1.85
7859 jmc 1.1203 checkpoint46f_post (2002/09/16)
7860 heimbach 1.85 o Enable tangent linear (forward mode) gradient checks:
7861     - extended active file handling to g_... files
7862     - added TANGENT_SIMULATION to theSimulationMode
7863     - extended grdchk package accordingly
7864     o added tangent linear setup in verification/carbon/code_ftl
7865     o added adjoint setup in verification/front_relax/code_ad
7866 mlosch 1.82
7867 jmc 1.1203 checkpoint46e_post (2002/09/05)
7868 mlosch 1.83 o Added new equation of state -> MDJWF
7869     - EOS of McDougall et al., 2002, JAOT, submitted
7870     - caveat: the equation of state is only valid for a smaller (more
7871     realistic?) range of values than JMD95P/Z and UNESCO
7872     - added masks to the calculation of pressure in store_pressure
7873     - added more check values for density in check_eos (ini_eos.F), some of
7874     the old check values are out of the range of the MDJWF-eos, so don't
7875     expect perfect matches for those
7876 jmc 1.1203 checkpoint46e_pre (2002/08/19)
7877 mlosch 1.83
7878 jmc 1.1203 checkpoint46d_post (2002/08/19)
7879 mlosch 1.82 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
7880     'OCEANICP', also initialised field pressure correctly in ini_eos in the
7881     case of pressure coordinates. eosType='JMD95Z' in
7882     combination with buoyancyRelation='OCEANICP' now causes an error.
7883     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7884     in find_alpha/beta.
7885 jmc 1.1203 checkpoint46d_pre (2002/08/15)
7886 mlosch 1.82
7887     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7888     so that JMD95Z and JMD95P give approptiate static stability in find_rho.
7889 adcroft 1.81
7890 jmc 1.1203 checkpoint46c_post (2002/08/15)
7891 adcroft 1.81 o Changes necessary for ocean in p-coordinates
7892     - Added new buoyancy relation = 'OCEANICP'
7893     - Added new parameters = gravitySign (this used to be contained inside
7894     the factor dRdZ which I added when we first switched to R coordinates).
7895     X GM/Redi is not compatible (yet)
7896     X bottom drag and no-slip need to be debugged.
7897 jmc 1.1203 checkpoint46c_pre (2002/08/07)
7898 mlosch 1.80
7899 jmc 1.1203 checkpoint46b_post (2002/08/07)
7900 mlosch 1.80 o Added new equation of state -> JMD95Z and JMD95P
7901 mlosch 1.83 - EOS of Jackett and McDougall, 1995, JAOT
7902 mlosch 1.80 - moved all EOS parameters into EOS.h
7903     - new routines ini_eos.F, store_pressure.F
7904     o Added UNESCO EOS, but not recommended because it requires
7905     in-situ temperature (see JMD95)
7906     o Modified formatting for knudsen2.f in utils/knudsen2 and added
7907     unesco.f to be used with POLY3
7908 jmc 1.1203 checkpoint46b_pre (2002/07/31)
7909 mlosch 1.79
7910 jmc 1.1203 checkpoint46a_post (2002/07/31)
7911 mlosch 1.79 o Added (atmospheric) pressure loading
7912     - new field in FFIELDS.h, etc...
7913     - new cpp flag ATMOSPHERIC_LOADING
7914     o Changed hFacC to _hFacC in calc_phi_hyd.F
7915     o Added SHORTWAVE_HEATING to some files for consistency
7916 jmc 1.1203 checkpoint46a_pre (2002/07/13)
7917 heimbach 1.78
7918 jmc 1.1203 checkpoint46 (2002/07/13)
7919 heimbach 1.78 further merges from release1_p5
7920     o new ctrl package
7921     - adopted from ECCO environment to enable optimization
7922     - added Eliassen Palm fluxes to controls
7923     o added Eliassen Palm flux controls to gradient check package
7924     o cost package
7925     - Compatible with new ctrl package
7926     - added Eliassen Palm cost hooks
7927     - modif's of existing cost functions
7928     o Adjoint-related bug fixes in kpp:
7929     - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
7930     - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
7931     o autodiff package
7932     - flow directives:
7933     + new for S/R do_the_model_io
7934     + enhanced for S/R checkpoint
7935     + new gmredi.flow
7936     - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
7937     disable adcommon.h/g_common.h by default.
7938     - fixed problem for adjoint of global_max
7939     o modified verification/carbon/
7940     o New setup for adjoint of global_ocean
7941     o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
7942     o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
7943     o incorporated hooks for sponge layer code (external_forcing.F)
7944    
7945 jmc 1.1203 checkpoint45d_post (2002/07/12)
7946 jmc 1.77 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
7947 jmc 1.76 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
7948     (affects plume_on_slope "cg2d" output)
7949 jmc 1.77 o add new parameter deltaTfreesurf for free-surface time stepping
7950     o exchange gT,gS when using staggerTimeStep & GM & Oly<4
7951 jmc 1.75 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
7952 jmc 1.74 o change phiMin in exp1 (to agree with documentation)
7953     o add new flags:
7954     - T,S forcing inside/outside Adams-Bashforth
7955     - turn off temp,salt advection and/or forcing
7956     - for each tracer, define internal flag for multiDimAdvection & A-B
7957     o monitor: change definition of KE to check conservation of Energy
7958 heimbach 1.73
7959 jmc 1.1203 checkpoint45c_post (2002/05/30)
7960 heimbach 1.73 o Removed f90 comments ("!")
7961     o Modified initialisations to enable exf package for MITgcm
7962     (without invoking ECCO_PACKAGE).
7963     o modifications to gradient check package (Martin Losch)
7964     - enable centered differences
7965     - modified format of standard output
7966 heimbach 1.72
7967 jmc 1.1203 checkpoint45b_post (2002/05/30)
7968 heimbach 1.72 o cleaned exchange calls in cg2d
7969     o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
7970     o included CPP option SINGLE_LAYER_MODE in thermodynamics
7971     to configure barotropic setup (Martin Losch)
7972     o moved some initialisations within bi,bj loop in dynamics
7973     (TAF flow dependency)
7974     o in initialise_varia, moved call packages_init_variables
7975     before convective_adjustment_init
7976     (corresponding adjustment of TAF tape initialisation).
7977     o in calc_diffusivity/calc_viscosity extended domain to full overlap.
7978 jmc 1.70
7979 jmc 1.1203 checkpoint45a_post (2002/05/01)
7980 jmc 1.71 o compute Rho over the whole domain (extend iMin,jMin indices)
7981     o specific exchange for X-slice domain (case Ny=1)
7982 jmc 1.70 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
7983     o solve_for_pressure : set cg2d_x to zero where OBCS are applied
7984 jmc 1.67
7985 heimbach 1.69 checkpoint44h_post = checkpoint45
7986     o Fix to restore differentiability:
7987     place at which packages_init_variables is called in
7988     initialise_varia is crucial for reverse control flow.
7989     o modifications in GMRedi to enable stable adjoint
7990     (corresponding modif's in thermodynamics, dynamics)
7991     o added missing hook for sponge layer code in external_forcing
7992     o modified test cost functions
7993     o storing in gad_advection (plus removal of write(0,*)!
7994     o missing headers TR1.h added in convective_adjustment routines
7995     o errorMessageUnit set non-equal zero in eeboot
7996     (conflict on some platforms, e.g. IBM SP3)
7997     o modified carbon verif.
7998    
7999 jmc 1.1203 checkpoint44h_pre (2002/03/14)
8000 jmc 1.68 o vertical grid option: allow to put the Interface at the middle between
8001     2 cell-centers ; replace delZ in pkg/kpp by drF.
8002 jmc 1.67 o GM Advective form: Tracers are advected using the residual transport (=
8003     Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
8004 jmc 1.66
8005 jmc 1.1203 checkpoint44g_post (2002/03/05)
8006 jmc 1.66 o fix surface correction term in multiDimAdvection (affects plume_on_slope
8007     results) ; ifdef missing in thermodynamics.F
8008 adcroft 1.65
8009     checkpoint44f_pre,checkpoint44f_post
8010     o added PTRACERS package
8011     This allows an arbitrary number of passive tracers to be integrated
8012     forward simultaneously with the dynamicaly model.
8013     + Implemented so far:
8014     - basic forward algorithm (time-stepping, advection, diffusion, convection)
8015     - I/O and checkpointing
8016     - GM/Redi *but* using the GM/Redi coefficient of Salt
8017     + Not implemented so far:
8018     - KPP
8019     - OBCS
8020     + No specific example supplied (yet) but global_ocean.90x40x15 has the
8021     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
8022     line in data.pkg.
8023     + This package is disabled by default since it increases storage.
8024    
8025 jmc 1.60
8026 adcroft 1.64 o testscript: added -cleanup option
8027 jmc 1.63 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
8028     b) enable to filter 2D fields.
8029 adcroft 1.62
8030     checkpoint44e_pre,post
8031     o re-wrote convective adjustment to use pre-calculated weights
8032     Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
8033     Adds: model/src/convective_weights.F, convectively_mixtracer.F
8034     Original calls to convect() still in place.
8035 heimbach 1.61
8036     chkpt44d_pre,post
8037     o added missing EXCLUDE_MONITOR flags
8038     o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
8039     (incompatible typ in MIN/MAX expressions caused problems
8040     on IBM SP3)
8041     o in genmake added variable MAKEDEPEND
8042     plus resetting for case SunOS
8043     o added timer_stats.c routine for IBM SP3
8044     o removed variables in dynamics
8045     !!! I forgot to create tag chkpt44d_pre !!!
8046     !!! But chkpt44d_pre = chkpt44c_post !!!
8047 jmc 1.63
8048     o real fresh water flux implemented with non-linear free-surface.
8049 heimbach 1.58
8050 jmc 1.59 chkpt44c_pre,post
8051     o few fix (mask in shap_s2, EmPmR in external_field_load,
8052     USE_NATURAL_BCS in solve_for_P);
8053     o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
8054    
8055 heimbach 1.58 checkpoint44b_pre/_post
8056     o merge of relevant stuff from the ecco-branch:
8057     - genmake: removed $S64 overwrite for case SunOS
8058     - pkg/exf: update and corrections for field swapping and obcs
8059     - pkg/ecco: parameter lists for the_model_main, the_main_loop
8060     harmonized between ECCO and MITgcm
8061     - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
8062     updated checkpointing_lev... lists for obcs
8063     - model/src: minor changes in forward_step, plot_field
8064     added directive for divided adjoint in the_main_loop
8065     - pkg/mdsio: added mdsio_gl_slice
8066 jmc 1.57
8067     o check parameters & config (chkpt44a_pre,post)
8068 jmc 1.56 o OBC and NonLin_FrSurf.
8069    
8070 jmc 1.1203 checkpoint44 (2002/01/18)
8071 jmc 1.54 o fix bug in mom_vi_del2uv
8072 jmc 1.56 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
8073     o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
8074     o update AIM experiments (NCEP input files)
8075     o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
8076 heimbach 1.55 o added some stuff for AD
8077 adcroft 1.53
8078 jmc 1.1203 checkpoint43 (2001/09/28)
8079 adcroft 1.53 o added two new advection tests
8080     o added global 4x4 degree ocean test
8081     o added test of H&S94 with free surface on cube
8082     o some final mods for gradient check, adjoint,...
8083 heimbach 1.52
8084 jmc 1.1203 checkpoint42 (2001/09/27)
8085 heimbach 1.52 Fixed AD-related problems:
8086     o Store directives up-to-date with re-arranged Adams-Bashforth
8087     (mainly thermodynamics.F)
8088     o New store directives for multi-dim. advection schemes
8089     * new CPP flag ALLOW_MULTI_DIM_ADVECTION
8090     * new common block and key passkey
8091     (mainly gad_advection.F)
8092     o Modified store directives for split of dynamics/thermodynamics
8093     for the case ALLOW_KPP
8094     o Cleaned argument list for timestep_tracer.F
8095 adcroft 1.51
8096 jmc 1.1203 checkpoint41 (2001/09/27)
8097 adcroft 1.51 o re-formatted/added comments in prologues of key subroutines
8098     to work with protex
8099 heimbach 1.47
8100 jmc 1.1203 checkpoint40 (2001/09/27)
8101 adcroft 1.50 o moved calc_gs, calc_gt and calc_tr1 back to model/src
8102     o added FLT (floats) package from Arne along with demo. experiment
8103     o re-arranged Adams-Bashforth scheme for tracers to allow easier
8104     implementation of forward-in-time forcing terms
8105     o more mods for non-linear free-surface including new variable
8106     o modified multi-dim method to work on cube
8107     o bug fix in KPP (from DM)
8108    
8109 jmc 1.1203 checkpoint40pre9 (2001/09/27)
8110 adcroft 1.49 o added DST advection schemes
8111     o fix MPI bug on SGI's
8112     o modifications for non-linear free-surface
8113     o fixed conditionals for fixed flow/passive tracer only mode
8114     o added tension/strain form of stress tensor
8115     o changes to commenting of arguments for TAF/TAMC
8116     o added/updated many matlab scripts
8117 adcroft 1.50 o added multi-dimensional advection method for tracers
8118 adcroft 1.49
8119 jmc 1.1203 checkpoint40pre8 (2001/09/05)
8120 heimbach 1.47 o new package rw/
8121     Added method for dumping intermediate local arrays:
8122     mdsio_writetile - same as mdsio_writefield except works from inside
8123     bi,bj loop
8124     mdsio_writelocal - same as mdsio_writetile except works for local
8125     arrays
8126     write_local_r? - higher-level wrapper for mdsio_writelocal
8127     Controlled by diagFreq. Defaults to zero (ie. no dumps)
8128     Example given at end of mom_vecinv.F that dumps some local arrays.
8129     o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
8130     control flux-form versus vector invariant code.
8131     Switch is runtime flag vectorInvariantMomentum (defaults to false)
8132     or genmake -DISABLE ...
8133     o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
8134     (additional storing is now needed for case vecinv;
8135     currently nothing implemented to switch this storing off
8136     in case fluxform is used since no CPP flag available).
8137 heimbach 1.46
8138 jmc 1.1203 checkpoint40pre7 (2001/08/14)
8139 heimbach 1.46 o bug fix in dynamics.F
8140     calc_viscosity called before k=1,Nr loop.
8141     o added some #ifdef's ALLOW_PASSIVE_TRACER
8142     o cleaned initialisations in ctrl_map_ini
8143     related to TAF
8144 heimbach 1.45
8145 jmc 1.1203 checkpoint40pre6 (2001/08/13)
8146 heimbach 1.45 o split dynamics into thermodynamics & dynamics
8147     o corresponding split of calc_diffusivity into
8148     calc_diffusivity, calc_viscosity
8149     (kpp_calc_diff, kpp_calc_visc).
8150     o Added diffkr, kapgm to control variables
8151     o bug fix in gmredi_slope_limit for ldd97
8152 adcroft 1.44
8153 jmc 1.1203 checkpoint40pre5 (2001/07/31)
8154 adcroft 1.44 o proper initialization of Adams-Bashforth time stepping
8155     + uses forward step for very first step of model (iter=0)
8156     o re-generated *all* output since almost all output is modified by this
8157     change (sorry but we've been putting this one off for about 2 years)
8158     + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
8159     *not* regenerated since they are already out of date and I don't
8160     want to create the impression that they are suddenly working.
8161     o removed KAP stuff for DEC's
8162     o modified/added many .cvsignore files in */code and */input
8163     o added new expt "solid-body.cs-32x32x1"
8164     + this uses an alternative form of ini_curvilinear_grid.F which
8165     is not necessarily any better than the current one...
8166 heimbach 1.43
8167 jmc 1.1203 checkpoint40pre4 (2001/07/30)
8168 heimbach 1.43 o added re-initialisations of utrans,vtrans,rtrans in
8169     calc_common_factors which are crucial for TAF.
8170     o extended iMin,jMin range for calc_common_factors,
8171     calc_diffusivity
8172     o added option ALLOW_PASSIVE_TRACER
8173     o a few minor updates and fixes
8174    
8175 jmc 1.1203 checkpoint40pre3 (2001/07/13)
8176 heimbach 1.42 o created calc_gtr1.F for gad package
8177     o split the_main_loop and re-introduced forward_step
8178     o some recomputations of nIter0 for TAMC
8179    
8180 jmc 1.1203 checkpoint40pre2 (2001/07/13)
8181 heimbach 1.41 o Updated to latest branch of AJA, JMC
8182     o Added gradient check package
8183     o Added routines for passive tracer handling
8184     o Added carbon sequestration sensitivity experiment
8185    
8186 jmc 1.1203 checkpoint39 (2001/05/14)
8187 heimbach 1.39 o Modifications and fixes to support TAMC
8188     (mainly missing or wrong directives)
8189     o Corrected common blocks when fooling TAMC to produce adjoint I/O
8190     in addummy_in_stepping
8191     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
8192     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
8193     o Included following packages:
8194     cal: calendar
8195     exf: external forcing
8196     ecco: essential routines to control use of cal, exf
8197     (NB: this is not the full ECCO environment)
8198 heimbach 1.40 o disabled some packages by default in genmake
8199 heimbach 1.39
8200 jmc 1.1203 checkpoint38 (2001/04/10)
8201 heimbach 1.38 o see notes_c37_adj.txt
8202     o corrected wrong layer index in external_forcing_t
8203     o replaced the_main_loop/forward_step by the_main_loop
8204     o removed forceoutput from write_state
8205     (replaced criteria for initial/final state)
8206     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
8207 jmc 1.36
8208 jmc 1.1203 checkpoint37 (2001/03/13)
8209 jmc 1.37 o mdsio.F routine split and packaged in pkg/mdsio
8210     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
8211     used unless genmake -disable=mdsio)
8212     o allow a more precise surface-geopotential gradient for the atmosphere
8213     taking into account the change in space of Alpha (=1/rho) at the surface.
8214     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
8215     (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
8216     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
8217     Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
8218     [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
8219     o Time-Average diagnostics defined as a pseudo package "timeave".
8220     o pickup files : old pickup (before c35) did not work with new code (c35
8221     and after) unless activating 2 commented lines in initialise-varia.
8222     o Non-Hydrostatic pickup file Pb fixed.
8223     o bug with Rigid-lid version (since c35) fixed.
8224    
8225 jmc 1.1203 checkpoint36 (2001/02/20)
8226 jmc 1.37 o implement Crank-Nickelson barotropic time-stepping
8227 jmc 1.36 o recover Time-Average diagnostics
8228     o fix Pb in checkpoint (PR#19)
8229     o AIM become a standard package ; clean unused CPP_kees
8230 jmc 1.35
8231 jmc 1.1203 checkpoint35 (2001/02/08)
8232 jmc 1.35 o subtantial rewrite of dynamics.f
8233     o allows staggered time-stepping
8234     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
8235     o added bottom drag (linear + quadratic)
8236 heimbach 1.33
8237 jmc 1.1203 checkpoint34 (2001/01/30)
8238 heimbach 1.33 o Modified exchange routines for correct reverse simulation.
8239     o Added verification output to comply with bug fix in impldiff.F
8240     as of c33 (exp2, natl_box).
8241     o Corrected store directives in dynamics.F
8242     o Corrected array boundaries in impldiff.F
8243     o Corrected array dimensions in gmredi.
8244     Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
8245 heimbach 1.34 o Added routine GLOBAL_SUM_INT to global_sum.F
8246 heimbach 1.33 o Added mdsio_gl.F for ECCO purposes.
8247 adcroft 1.32
8248 jmc 1.1203 checkpoint33 (2000/11/30)
8249 adcroft 1.32 o Fixed bug in lower BC in impldiff.F
8250     o Fixed confusion about units of forcing arrays in FFIELDS.h
8251     namely Fu,Fv,Qnet,Qsw,EmPmR:
8252     - Removed verification/natl_box/code/external_fields_scale.F
8253     (did not differ from that in model/src)
8254     - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
8255     (see FFIELDS.h for description)
8256     - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
8257     kpp_calc.F and kpp_transport_t.F
8258     - Removed model/src/external_fields_scale.F and calls to it
8259     - verification/natl_box uses flux data with "atmospheric" sign so
8260     a special version of external_fields_load.F is used to
8261     change the data as it's read in. This way, the arrays
8262     have the right units and signs at all times tha a user could
8263     possibly use them.
8264     o Corrected genmake to delete a temporary file during configuration
8265 heimbach 1.31
8266 jmc 1.1203 checkpoint32 (2000/11/13)
8267 heimbach 1.31 o Scaling of forcing fields moved from external_forcing.F to
8268     external_fields_scale.F, called directly after loading fields.
8269     o Surface relaxation terms added to surface tendency fields in
8270     extra subroutine.
8271     o impldiff.F changed to avoid storing by TAMC of huge intermediate
8272     fields.
8273     o Changes in GMRedi to comply with packaging structure.
8274     o Modifications and bug fixes in KPP package.
8275     o Verification experiment for KPP added (verification/nat_box/)
8276 heimbach 1.30
8277 jmc 1.1203 checkpoint31 (2000/09/11)
8278 heimbach 1.30 o Packages interface brought in line with defined standard
8279     -> new routines packages_...F
8280     -> changes in initialise_fixed.F, initialise_varia.F
8281     -> enables initialisation interface for ECCO package
8282     o Rescaling of external forcing fields immediately after read
8283     (removed from external_forcing.F)
8284     -> new: surface_fields_scale.F
8285     -> affects ini_foorcing.F, external_fields_load.F
8286     o Computation of surface tendencies before tendency updates.
8287     -> new: external_forcing_surf.F
8288     o Change of variable names useGMRedi, useKPP, useECCO
8289     o Further changes in dynamics.F, impldiff.F for TAMC
8290     o Tested for experiments 0, 2, 4.
8291     - not yet tested for GMRedi.
8292     - not yet tested for KPP.
8293 adcroft 1.29
8294 jmc 1.1203 checkpoint30 (2000/07/13)
8295 adcroft 1.29 o Updates for OBCs
8296     o New experiment for test OBCs (internal_wave)
8297     o New output.txt in verification/exp4/results/
8298     o Updates for KPP: calculation of viscosity corrected, new variables
8299     kpp_dumpFreq and kpp_taveFreq
8300     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
8301     and entry for T90 in genmake
8302 adcroft 1.28
8303 jmc 1.1203 checkpoint29 (2000/06/21)
8304 adcroft 1.28 o packaged KPP and GM/Redi
8305 heimbach 1.27
8306 jmc 1.1203 checkpoint28 (2000/06/09)
8307 heimbach 1.27 o Corrected initialization of hFacMin for difference vertical coordinates
8308     o Modified calculation of partial cell thickness to more robust algorithm
8309     o config_summary.F: replaced write_1D_... by write_0D_...
8310     read_write.F: added subroutines write_0D_...
8311     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
8312     included some initialisations required for TAMC.
8313     o routine calc_isoslopes: modified sqrt computation to make it
8314     differentiable for zero argument.
8315     o routines dynamics, impldiff:
8316     included store directives and tape key computations required for TAMC.
8317     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
8318 adcroft 1.26
8319 jmc 1.1203 checkpoint27 (2000/04/10)
8320 adcroft 1.26 o fixed calc_isoslopes() to so that cancellation of terms in tensor
8321     formulation works properly with variable resolution.
8322     o restructured the calling tree between the_model_main() and dynamics()
8323     o split initialise() into initialise_fixed() and initialise_varia()
8324     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
8325     in new routine ini_psurf()
8326 adcroft 1.25
8327 jmc 1.1203 checkpoint26 (2000/04/05)
8328 adcroft 1.25 o moved some #ifdef in optional routines to encompass everything
8329     except the argument declarations. This was using up some memory.
8330     o fixed macros like _ADT to work with both versions of Linux cpp
8331     o cleaned up some unused and uninitialized variables
8332     (helps when debugging with strict compile options)
8333     o split up CPP_EEOPTIONS.h into options and macros
8334     (macros are now in eesupp/inc/CPP_EEMACROS.h)
8335     o patch for 2 processor JAM mode
8336 adcroft 1.24
8337 jmc 1.1203 checkpoint25 (2000/03/15)
8338 adcroft 1.24 o updates for OBCs and NH
8339     o dramatically reduced memory usage
8340     o added "JAM" routines for use on Artic network
8341     o parameterization of convection by implicit vertical diffusion
8342     o added a diagnostic of convective index
8343     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
8344     (this is was partly for OBCs and NH but also in anticipation of
8345     an explicit free-surface option)
8346     o initial state input files for U and V
8347 adcroft 1.23
8348 jmc 1.1203 checkpoint24 (1999/08/02)
8349 adcroft 1.23 o Removed some spurious "REAL"s
8350     o Updated KPP to latest version from JPL
8351     o Added a COS(latitude) in horizontal viscosity
8352 adcroft 1.22
8353 jmc 1.1203 checkpoint23 (1999/05/26)
8354 adcroft 1.22 o Added del^4 diffusion for salt and temperature
8355     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
8356 adcroft 1.21
8357 jmc 1.1203 checkpoint22 (1999/05/18)
8358 adcroft 1.21 o Made many small changes: implicit none, format(i5), etc...
8359     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
8360 adcroft 1.20
8361 jmc 1.1203 checkpoint21 (1999/05/18)
8362 adcroft 1.20 o Introduced new I/O package that supports direct-access records (mdsio.F)
8363     o Split-up mid-level I/O routines
8364     o Updated input data for experiments 0,1,2,4 and 5
8365     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
8366 adcroft 1.18
8367 jmc 1.1203 checkpoint20 (1999/03/22)
8368 adcroft 1.19 o Tidied up open-boundaries some more
8369     o Added non-hydrostatic code
8370     o Fixed some input data
8371     o Modified MPI start-up to work in "coupled" context.
8372    
8373 jmc 1.1203 checkpoint19 (1998/12/15)
8374 adcroft 1.18 o Tidied up directory structure for verification experiments.
8375     o Added new code for open boundaries.
8376     o Corrected advective terms near boundaries.
8377     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
8378     o Implemented free-slip/no-slip BCs and del^4 dissipation.
8379 adcroft 1.19 o Split default parameters out of ini_parms.F into set_defaults.F.
8380 cnh 1.17
8381 jmc 1.1203 checkpoint18 (1998/11/30)
8382 cnh 1.17 o Further changes for optional code generation with
8383     CPP - ugh!
8384 cnh 1.16
8385 jmc 1.1203 checkpoint17 (1998/11/03)
8386 cnh 1.16 o Beginning to incorporating modularity
8387     for supporting atmos. and ocean configs.
8388     o Small changes for TAMC complinace
8389     o New ultra simple test case. Barotropic box
8390     configuration "exp0".
8391 cnh 1.15
8392 jmc 1.1203 checkpoint16 (1998/10/28)
8393 cnh 1.15 o Minor changes to exchange routines to support
8394     accumulation in reverse mode. Adjoint of an
8395     assignment is an addition.
8396     o Changes to support compilation by TAMC (LR(1)
8397     syntax) and by g77 under Linux ( 72 character
8398     limit ).
8399 cnh 1.14
8400 jmc 1.1203 checkpoint15 (1998/09/29)
8401 cnh 1.14 Rewrote exchange routines to allow
8402     o General tile <-> tile connectivity.
8403     o TAMC reverse mode flag ( is this really needed? )
8404     o Variable width overlap and exchange region widths.
8405     o Hooks for sharing data via DMA, Arctic, Memory Channel,
8406     shmput/shmget, VIA, SYSV shmem and every other cool
8407     communication method.
8408 cnh 1.13
8409 jmc 1.1203 checkpoint14 (1998/09/09)
8410 cnh 1.13 Consistent isomorphism chages made. These allow dynamical core
8411     to support both pressure and meters as a vertical coordinate.
8412 cnh 1.12
8413 jmc 1.1203 checkpoint13 (1998/07/17)
8414 cnh 1.12 Release which corrects global_max problem and a couple
8415     of KGM time-averaging diagnostic errors. Also contains
8416     a double-gyre experiment setup as well as the baseline
8417     4 degree global template. The double gyre template is
8418     organised to allow it to be applied automatically to
8419     the baseline configuration.
8420 adcroft 1.11
8421     branch-point-rdot
8422     A few tidy-ups have been made bt the real point of this
8423     check-point (excuse the pun) is to allow a branch to be
8424     made for the purposes of adding the rDot alterations.
8425     I don't want to commit the rDot to the main-trunk until
8426     we've actually tested it...
8427 cnh 1.10
8428 jmc 1.1203 checkpoint12 (1998/07/08)
8429 cnh 1.10 Tidy up and added generic genmake script (formerly
8430     configure script).
8431     Released to testers.
8432 adcroft 1.9
8433 jmc 1.1203 checkpoint11 (1998/07/02)
8434 adcroft 1.9 Re-arranged initialise() and introduced ini_vertical_grid()
8435     and ini_masks_etc().
8436 adcroft 1.8
8437 jmc 1.1203 checkpoint10 (1998/07/01)
8438 adcroft 1.8 Introduced the configure script.
8439     Separated out the diags package.
8440     Added template for writing time-averages of tile/intermediate quantities.
8441     Updated SIZE.h in exp2 and made the data big-endian.
8442 adcroft 1.7
8443 jmc 1.1203 checkpoint9 (1998/06/22)
8444 adcroft 1.7 MPI fix. Filename changes (meta/data). salbin*y stuff.
8445     General tidy-up.
8446     SST.bin SSS.bin added to verification/exp2
8447 adcroft 1.6
8448 jmc 1.1203 checkpoint8 (1998/06/22)
8449 adcroft 1.6 Inludes time-dependant forcing and time-averaging.
8450     Works at 4x4 and 2.8125x2.8125 global
8451    
8452     checkpoint7-4degree-ref
8453     Branch from checkpoint7. Released for application to
8454     global modeling and general modeling - process studies, regional
8455     model etc..
8456     Configured for verification/exp2 - 4 degree global, two process.
8457 cnh 1.5
8458 jmc 1.1203 checkpoint7 (1998/06/15)
8459 cnh 1.5 Created by cnh
8460     Simple 4 degree global simulation
8461     configuration.
8462     Includes climatological wind,
8463     hydrography, bathymetry etc
8464     Does not include Heat Flux and E-P
8465 cnh 1.4
8466 jmc 1.1203 checkpoint6 (1998/06/08)
8467 cnh 1.4 Created by cnh
8468     merged checkpoint5 with CD and
8469     spherical polar code.
8470     Still some problems with GM Redi
8471     abd full topography.
8472 cnh 1.3
8473 jmc 1.1203 checkpoint5 (1998/06/08)
8474 cnh 1.3 Created by AJA
8475     contains updates to GM Redi
8476     and reordered timestepping loop
8477     for Implicit Diffusion.
8478 cnh 1.2
8479 jmc 1.1203 checkpoint4 (1998/05/30)
8480 cnh 1.2 Created by cnh
8481     Contains memory saving macros ( _rdxc etc..) for when
8482     grid variations are limited.
8483     Contains polynomial coeffs for EOS and knudsen program
8484     for generation.
8485    
8486 jmc 1.1203 checkpoint3 (1998/05/26)
8487 cnh 1.1 Created by cnh
8488     Added extra flags for runtime options
8489     Added this file
8490     Added implicit free-surface
8491     Added pre-conditioner
8492     Put compare01 into repository ( compare01/... )
8493     Put data and eedata into repository ( verification/exp1 )
8494    
8495     checkpoint2
8496     Created by AJA
8497     Added GM/Redi
8498    
8499     checkpoint1
8500     Created by AJA
8501     Restructured kloop in dynamics.F
8502     Added non-linear EOS
8503    
8504 cnh 1.2 baseline
8505     Original checked in code
8506 cnh 1.1

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