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revision 1.1315 by heimbach, Sat Oct 16 19:33:41 2010 UTC revision 1.1386 by heimbach, Sat Mar 5 17:58:22 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint62t (2011/03/05)
8    o pkg/obcs:
9     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
10       then normal component. This ensures that the normal component is set
11       correctly even when it conficts with tangential setting from an other OB.
12       Affects results of test-experiment seaice_obcs: update the output.txt
13    o pkg/obcs:
14     - add code to monitor statistics of dynamical fields at OB.
15     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
16       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
17       - change default: balance the Net inflow through all OB (instead of balancing
18         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
19     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
20       to match Nortern OB inflow (OBCS_balanceFacN=0).
21    o pkg/seaice:
22     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
23    o pkg/seaice (seaice_growth v 1.113):
24     - reverting seaice_growth to v 1.111 in order to have code with exact bit
25       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
26       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
27       runtime flag SEAICEareaFormula is kept but is inactive
28    o model/src:
29     - add new param to scale curvilinear grid distance and area when using
30       a different sphere radius from the grid-files.
31     - test/check multi-threads EXCH applied to local variable (cg2d_x)
32    o adjoint:
33     - enable adjoint of Stevens OB
34     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
35       (a bit delicate because of potentially modified adj. common block structure;
36       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
37    
38    checkpoint62s (2011/02/15)
39    o pkg/seaice (seaice_growth v 1.112):
40     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
41       computing the ice cover tendency from effective thickness tendencies. Include
42       Ian Fenty's formula.
43     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
44       SEAICEareaFormula.
45     - simplify notations for the various d_HEFF/d_AREA terms.
46    o pkg/gmredi:
47     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
48       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
49       add a verification test-run (front_relax.bvp) to test GM_useBVP.
50    o pkg/seaice (seaice_growth v 1.111):
51     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
52     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
53       also melt ice.
54    o pkg/seaice:
55     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
56     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
57    o pkg/cheapaml:
58     - from Nico Wienders: New version of this package.
59    o pkg/flt:
60     - add CPP options to prevent floats to re-enter the opposite side of
61       a periodic domain (default: keep periodicity)
62    o pkg/gmredi:
63     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
64       (needed for multi-dim advection).
65     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
66    o model/src:
67     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
68    o tutorial_tracer_adjsens
69     - extend to NLFS and replace maskC by hFacC
70       (change reference output accordingly)
71    
72    checkpoint62r (2011/01/24)
73    o testreport:
74     - add option -deloutp (-do) to remove output file after successful run
75     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
76       extract exact list of procs from this file ; adjust COMMAND by
77       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
78    o pkg/ecco: replace old ineffective way of penalizing deviations from
79      first guess (of obcs) with code by Matt Mazloff
80    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
81      exf/cal
82      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
83        and handle case of obcs?period == 0
84        Not affected by these changes: There is still an inconsistency in
85        the computation of start/endrec for the obcs variables for ALLOW_CAL
86        defined (see comment by Menemenlis, 7-Mar-2003)
87      - make S/R ctrl_get_gen_rec return something meaningful even if
88        ALLOW_CAL is not defined
89      - ctrl_getobcs?: simplify code so that it does not need to use
90                       S/R exf_swapfields
91    o testreport:
92       allow to test MPI with different number of processors for each experiment:
93       create file "SIZE.h.mpi" in each build dir.
94       Note: update of "-command" argument not yet implemented.
95    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
96      alleviate the need for additional 3D tapes when using
97      the non-inear free surface in the adjoint. This is done
98      by adding an 'update' of hfacc etc. to their current
99      value at the beginning of forward_step.F.
100    o pkg/seaice
101      seaice_lsr: move stress-divergence computations out of outer pseudo-
102      timestepping loop
103    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
104      up, so that the calls of the ctrl_* subroutines are really at the end
105      of the routine.
106    o pkg/gmredi:
107      allow to specify a 2-D horizontal map and a 1-D vertical profil
108      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
109    o pkg/seaice:
110      move lsr iterations from seaice_dynsolver to seaice_lsr.
111    o pkg/seaice:
112      reduce memory footprint of seaice mutldim advection tapes,
113      by using a 2D tape independent of the generic_advdiff ones,
114      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
115    
116    checkpoint62q (2010/12/29)
117    o model/src:
118      - check horizontal grid-spacing for unset or zero/negative values.
119      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
120    o pkg/flt:
121      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
122      - precision of input and output files set according to readBinaryPrec
123        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
124      - initial float position from tiled file was not converted to index space
125        (looks like a bug): fixed to make it similar to initial pos. global file.
126    o global_ocean.cs32x15:
127       change SIZE.h of AD set-up to get same tiling as with MPI.
128       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
129    o model/src:
130       add flag to control printing of domain fields (bathymetry, hFac ...) in
131       ini_mask_etc (call to plot_fieds_xy*).
132    o pkg/thsice:
133       if useEXF, some forcing fields are not valid in overlap: fixed by computing
134       over the interior only + apply EXCH at the end (like with SEAICE advection).
135    o pkg/mdsio:
136      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
137        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
138      - change barrier call for safe multi-threads access to 3-D shared buffer.
139      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
140      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
141        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
142    o pkg/flt:
143      - add fourth-order Runge-Kutta integration
144      - add basic exch2 support (only 1 facet supported so far!)
145    o pkg/mdsio+rw:
146      new S/R to read local (or tile independent) vector (read counterpart of
147       mds_writevec_loc, and front-end write_glvec_rl/rs).
148    o global_ocean.cs32x15: additional input_ad.seaice experiment
149        that uses pkg/seaice rather than pkg/thsice.
150        (using multidim advection for seaice)
151    o towards more F95 syntax for array specification in namelist:
152      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
153        of all verification experiments.
154           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
155          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
156      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
157    o global_ocean.cs32x15: additional input.seaice experiment
158        that uses pkg/seaice rather than pkg/thsice.
159    
160    checkpoint62p (2010/12/17)
161    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
162        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
163    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
164        allow for use of multim. advection in seaice adjoint.
165    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
166      - first attempt to close budgets by taking into account the freshwater
167        flux implied by the sublimation of snow and ice. So far only the
168        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
169        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
170    o eesupp/src:
171      new S/R with new option (NML_EXTENDED_F77) to change array specification
172      from F95 standard to commonly accepted extended F77 form.
173      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
174      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
175      for less tolerant f77 compiler (e.g., pgf77, g77).
176    o globalFiles:
177      commented out in parameter file "data" since it's not safe with MPI
178      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
179      in this case); no longer commented out in restart test (tst_2+2).
180    o add adTapeDir to specify a special directory where adjoint tapes are
181      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
182      and cannot be used together with mdsioLocalDir.
183    o nesting pkgs:
184      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
185      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
186      - add parameter files + utils dir + output from short run on beagle.
187    o pkg/seaice:
188        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
189    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
190      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
191    
192    checkpoint62o (2010/11/25)
193    o pkg/exf:
194      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
195    o pkg/seaice:
196      - seaice_ocean_stress: split a loop for better vectorization of the
197        adjoint code
198      - seaice_growth.F: fix bug in conservation of freshwater connected to
199        capping of heff, put contribution into d_HEFFbyNEG
200      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
201        by something more sensible (parameters that are what their name implies)
202      - change some defaults, so that by default exf-parameters are used for
203        things like rhoAir, cpAir,latent/sensible heat parameters, in order
204        to reproduce the old results, many data.seaice now contain funny values
205        for cpAir and latent heat of sublimation
206    o packages_readparms.F: move exf_readparms up in line so that
207        exf-parameters are visible for other packages (e.g. seaice)
208    o debugMode & debugLevel=2:
209      - differentiate between debugMode & debugLevel=2:
210        debugMode: controls printing of debug messages (sequence of S/R calls).
211        debugLevel: controls printing of algorithm intermediate results and stats.
212      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
213        => allows to print debug-stats without all sequence of call messages.
214      - switch control of debug print from debugLevel to debugMode in many S/R.
215    o pkg/obcs (obcs-sponge):
216        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
217        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
218    o pkg/generic_advdiff:
219      - record overlap minimum size for each advection scheme;
220      - refine criteria on overlap minimum size;
221      - check and stop (in gad_check) if overlap size is too small.
222    o pkg/obcs:
223      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
224        once, in ptracers_implicit.F)
225      - with seaice: remove test on empty file name in obcs_apply_seaice (always
226        apply OB values when tile has OB)
227    o model/src, coriolis setting:
228      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
229        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
230        files (selectCoriMap=3) with any grid.
231      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
232    o pkg/seaice/seaice_growth.F:
233        a few cosmetic changes that reduce the number of lines of code
234    o pkg/obcs: add boundary conditions following Stevens (1990)
235      - the code follows old MOM/NAOSIM code
236      - so far it is only implemented for the eastern and western boundaries
237        and NOT for pTracers
238    o pkg/rbcs:
239      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
240        beginning of the first rbcs forcing period.
241      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
242        offline package, i.e., one file per time, labeled by iteration number;
243        deltaTrbcs sets the timestep with which the data was generated;
244        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
245      - rbcsForcingCycle=0 makes forcing non-cyclic.
246      - make arithmetic safe for negative times and odd forcing periods.
247    
248    checkpoint62n (2010/11/09)
249    o pkg/seaice:
250        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
251    o pkg/obcs:
252       New S/R to copy tracer value from the OB location to narrow band region
253        (width = same as overlap) beyond the OB: preserve OB value (needed for
254        high-order scheme) which were overwritten by EXCH call if in overlap
255        region. Applied to theta, salt, ptracer and advected seaice variables.
256       With seaice: use maskInC in similar way as in gad_advection.F,
257        in seaice_advection.F and advect.F.
258       Update output of experiment seaice_obcs and change exp4 to test OBCS with
259        4th order Adv.Scheme. for pasive salt and ptracer.
260    o tools/genmake2:
261      - when looking for an optfile (not specified), only search for Fortran compiler
262        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
263      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
264        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
265      - set default for CPP to "cpp -traditional -P" (was the case without specifying
266        an optfile, but otherwise default was just "cpp".
267      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
268      - when "CC" is not set in the optfile, look for possible C compiler
269        (instead of just setting CC=cc)
270      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
271        => add a ".F" to ".o" rule for source files with no "#include" (such as
272           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
273      - move gfortran before g77 in list of possible Fortran compiler (consistent
274        with reference compiler switch from g77 to gfortran)
275    o pkg/seaice:
276      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
277        seaice_check that stops the model, when the CPP flag is used.
278      o seaice_growth.F: make capping of ice volume conserving by returning the
279        capped ice as freshwater to EmPmR. This does not change the verification
280        experiments but will change runs where the capping is acutally active
281    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
282      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
283         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
284         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
285    o tools/genmake2:
286      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
287      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
288      - clean previous genmake log files before anything else.
289      - change Makefile to remove testreport log files (*.tr_log) and genmake log
290        files only with "CLEAN" target (instead of "Clean");
291    o pkg/generic_advdiff:
292      Change OBCS in multiDim advection (gad_advection.F):
293       Use maskInC to prevent intermediate update of tracer-field in OB regions,
294       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
295       which were applying future time-step OB values.
296      This way, all explicit calculations use current-time-step OB values
297       (simpler and more consistent).
298      Affects results when set-up uses time-varying OBC and multi-dim advection;
299       update output of experiment seaice_obcs.
300    o pkg/seaice:
301      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
302       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
303         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
304      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
305       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
306       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
307    o pkg aim (2010/10/26):
308      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
309        formulation with obliquity, eccentricity, ... as run-time parameters,
310      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
311        upward shortwave radition at the surface (all-sky and clear-sky).
312    o pkg/obcs:
313      - writing sections with globalFiles=T does not work: switch to tiled-files
314        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
315      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
316      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
317    
318    checkpoint62m (2010/10/21)
319    o pkg/seaice: vectorize seaice_solve4temp.F
320      - move iterations loops outside of i/j-loops
321      - requires 2D arrays for TB and effConduct
322      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
323        modified in this routine
324      - a little bit of clean up, adjusting indentation, etc.
325      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
326        performance and '**TWO' by '**2' (because TWO is a float),
327        replaced ONE, ZERO
328  o eesupp/src:  o eesupp/src:
329     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
330  o pkg/seaice/seaice_growth.F  o pkg/seaice/seaice_growth.F
# Line 39  o pkg/thsice: Line 360  o pkg/thsice:
360      experiments that have this flag undefined (not tested in verification);      experiments that have this flag undefined (not tested in verification);
361      a little reorganization to save a few 2D fields and recomputations      a little reorganization to save a few 2D fields and recomputations
362    - 1st step of revisiting thsice adjoint (major recomp. sorted out)    - 1st step of revisiting thsice adjoint (major recomp. sorted out)
363      - 2nd step:  fix some store dirs
364        o seems to work somewhat, i.e. using ifort but not g77
365        o likely cause are incomplete init. or recomputation
366        o start verification/global_ocean.cs32x15/input_ad.thsice
367  o pkg/obcs: add support for exch2  o pkg/obcs: add support for exch2
368    - the position of the boundary and prescribed values are specified using    - the position of the boundary and prescribed values are specified using
369      a global domain with exch2 facets stacked      a global domain with exch2 facets stacked
# Line 400  o tools/build_options: Line 725  o tools/build_options:
725      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
726  o pkg/ecco  o pkg/ecco
727    - allow user defined cost function contributions    - allow user defined cost function contributions
728          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
729          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
730    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
731        the two options are complementary.        the two options are complementary.
732  o pkg/smooth  o pkg/smooth

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