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revision 1.1281 by jmc, Thu May 27 15:21:22 2010 UTC revision 1.1345 by mlosch, Mon Dec 6 10:52:52 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o add adTapeDir to specify a special directory where adjoint tapes are
8      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
9      and cannot be used together with mdsioLocalDir.
10    o nesting pkgs:
11      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
12      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
13      - add parameter files + utils dir + output from short run on beagle.
14    o pkg/seaice:
15        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
16    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
17      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
18    
19    checkpoint62o (2010/11/25)
20    o pkg/exf:
21      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
22    o pkg/seaice:
23      - seaice_ocean_stress: split a loop for better vectorization of the
24        adjoint code
25      - seaice_growth.F: fix bug in conservation of freshwater connected to
26        capping of heff, put contribution into d_HEFFbyNEG
27      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
28        by something more sensible (parameters that are what their name implies)
29      - change some defaults, so that by default exf-parameters are used for
30        things like rhoAir, cpAir,latent/sensible heat parameters, in order
31        to reproduce the old results, many data.seaice now contain funny values
32        for cpAir and latent heat of sublimation
33    o packages_readparms.F: move exf_readparms up in line so that
34        exf-parameters are visible for other packages (e.g. seaice)
35    o debugMode & debugLevel=2:
36      - differentiate between debugMode & debugLevel=2:
37        debugMode: controls printing of debug messages (sequence of S/R calls).
38        debugLevel: controls printing of algorithm intermediate results and stats.
39      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
40        => allows to print debug-stats without all sequence of call messages.
41      - switch control of debug print from debugLevel to debugMode in many S/R.
42    o pkg/obcs (obcs-sponge):
43        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
44        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
45    o pkg/generic_advdiff:
46      - record overlap minimum size for each advection scheme;
47      - refine criteria on overlap minimum size;
48      - check and stop (in gad_check) if overlap size is too small.
49    o pkg/obcs:
50      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
51        once, in ptracers_implicit.F)
52      - with seaice: remove test on empty file name in obcs_apply_seaice (always
53        apply OB values when tile has OB)
54    o model/src, coriolis setting:
55      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
56        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
57        files (selectCoriMap=3) with any grid.
58      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
59    o pkg/seaice/seaice_growth.F:
60        a few cosmetic changes that reduce the number of lines of code
61    o pkg/obcs: add boundary conditions following Stevens (1990)
62      - the code follows old MOM/NAOSIM code
63      - so far it is only implemented for the eastern and western boundaries
64        and NOT for pTracers
65    o pkg/rbcs:
66      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
67        beginning of the first rbcs forcing period.
68      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
69        offline package, i.e., one file per time, labeled by iteration number;
70        deltaTrbcs sets the timestep with which the data was generated;
71        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
72      - rbcsForcingCycle=0 makes forcing non-cyclic.
73      - make arithmetic safe for negative times and odd forcing periods.
74    
75    checkpoint62n (2010/11/09)
76    o pkg/seaice:
77        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
78    o pkg/obcs:
79       New S/R to copy tracer value from the OB location to narrow band region
80        (width = same as overlap) beyond the OB: preserve OB value (needed for
81        high-order scheme) which were overwritten by EXCH call if in overlap
82        region. Applied to theta, salt, ptracer and advected seaice variables.
83       With seaice: use maskInC in similar way as in gad_advection.F,
84        in seaice_advection.F and advect.F.
85       Update output of experiment seaice_obcs and change exp4 to test OBCS with
86        4th order Adv.Scheme. for pasive salt and ptracer.
87    o tools/genmake2:
88      - when looking for an optfile (not specified), only search for Fortran compiler
89        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
90      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
91        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
92      - set default for CPP to "cpp -traditional -P" (was the case without specifying
93        an optfile, but otherwise default was just "cpp".
94      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
95      - when "CC" is not set in the optfile, look for possible C compiler
96        (instead of just setting CC=cc)
97      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
98        => add a ".F" to ".o" rule for source files with no "#include" (such as
99           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
100      - move gfortran before g77 in list of possible Fortran compiler (consistent
101        with reference compiler switch from g77 to gfortran)
102    o pkg/seaice:
103      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
104        seaice_check that stops the model, when the CPP flag is used.
105      o seaice_growth.F: make capping of ice volume conserving by returning the
106        capped ice as freshwater to EmPmR. This does not change the verification
107        experiments but will change runs where the capping is acutally active
108    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
109      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
110         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
111         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
112    o tools/genmake2:
113      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
114      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
115      - clean previous genmake log files before anything else.
116      - change Makefile to remove testreport log files (*.tr_log) and genmake log
117        files only with "CLEAN" target (instead of "Clean");
118    o pkg/generic_advdiff:
119      Change OBCS in multiDim advection (gad_advection.F):
120       Use maskInC to prevent intermediate update of tracer-field in OB regions,
121       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
122       which were applying future time-step OB values.
123      This way, all explicit calculations use current-time-step OB values
124       (simpler and more consistent).
125      Affects results when set-up uses time-varying OBC and multi-dim advection;
126       update output of experiment seaice_obcs.
127    o pkg/seaice:
128      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
129       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
130         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
131      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
132       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
133       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
134    o pkg aim (2010/10/26):
135      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
136        formulation with obliquity, eccentricity, ... as run-time parameters,
137      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
138        upward shortwave radition at the surface (all-sky and clear-sky).
139    o pkg/obcs:
140      - writing sections with globalFiles=T does not work: switch to tiled-files
141        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
142      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
143      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
144    
145    checkpoint62m (2010/10/21)
146    o pkg/seaice: vectorize seaice_solve4temp.F
147      - move iterations loops outside of i/j-loops
148      - requires 2D arrays for TB and effConduct
149      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
150        modified in this routine
151      - a little bit of clean up, adjusting indentation, etc.
152      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
153        performance and '**TWO' by '**2' (because TWO is a float),
154        replaced ONE, ZERO
155    o eesupp/src:
156       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
157    o pkg/seaice/seaice_growth.F
158      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
159      merging process. The merged routine has two branches, and one activates the 'evolution'
160      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
161      In summary, here is what the '10/10 revision' did consist of
162        part 1: seaice_growth.F revisions 1.71 to 1.75
163          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
164            The emphasis here was on improving readability (e.g. by trying to use meaningful
165            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
166        part 1.5:
167          - revising the lab_sea experiment to make it a more useful (i.e. stable
168            and representative of an actual model run). This was done by generating a
169            (winter) pickup to start from, switching back the main experiment dynamic
170            solver from evp to lsr, having one of the experiments use the free drift solution.
171        part 2: seaice_growth.F revisions 1.76 to 1.85
172          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
173          - Sorting out the various fields units and sign (set early on and reset at the end)
174            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
175            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
176          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
177            and simplifying logical expressions to further improve readibility.
178        part 3: seaice_growth.F revisions 1.86 to 1.89
179          - Re-organize the blocks of code more logically.
180          - Merging the '_if.F' pieces that add something new.
181    o pkg/thsice:
182      - vectorize thsice_solve4temp and thsice_get_exf.
183        Problem: thsice_solve4temp has an unvectorizable statement that
184        might also be problematic for TAF
185      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
186        does not change the verifcation experiment, but will change all
187        experiments that have this flag undefined (not tested in verification);
188        a little reorganization to save a few 2D fields and recomputations
189      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
190      - 2nd step:  fix some store dirs
191        o seems to work somewhat, i.e. using ifort but not g77
192        o likely cause are incomplete init. or recomputation
193        o start verification/global_ocean.cs32x15/input_ad.thsice
194    o pkg/obcs: add support for exch2
195      - the position of the boundary and prescribed values are specified using
196        a global domain with exch2 facets stacked
197        - in x for N,S boundaries (like W2_mapIO=-1)
198        - in y for E,W boundaries (so E,W boundaries do not overlap)
199    o pkg/mdsio: add support for writing global sections with exch2
200        file layout is as for obcs described above:
201        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
202        - for y-z sections, facets are stacked in y
203    o pkg/thsice:
204       - change a few routines for better vectorization: thsice_albedo.F,
205         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
206         not affected, but in particular the latter routine has changed
207         dramatically (not necessarily easier to read now).
208       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
209       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
210    o verification/lab_sea:
211      - overhaul of the forward model experiments. The main motivation
212        for this revision is that lab_sea has proven quite fragile (when
213        changing the sea-ice code, and switching platforms) to a point
214        when failures were very hard to attribute to specific code problems.
215      - the suspected reason for this fragility is noise amplification by evp so,
216        to start with, we decided to replace evp with lsr in the main experiment.
217      - the input.lsr experiment thus became obsolete and was removed.
218      - it was replaced with the input.fd experiment that uses an
219        analytical "free drift" solution as the ice velocity field.
220      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
221        will hopefully allow us to discriminate problems due to dynamic solvers
222        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
223        us to test additional options, along with the salt plume package.
224      - Finally a pickup was generated (at the end of a one year run) to
225        make the tests more representative of an actual model run. Previously
226        the tests starting point was a 1m thickness of ice everywhere.
227    o pkg/seaice:
228      - introducing S\R seaice_freedrift.F that compute the
229        analytical solution to an approximate ice momentum
230        equation (i.e. the simple stress/coriolis balance).
231      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
232        of the free drift velocity field, and enable its use.
233        To actually use the free drift solution as the model ice
234        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
235    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
236    
237    checkpoint62l (2010/10/04)
238    o pkg/seaice:
239      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
240      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
241       version (with USE_ORIGINAL_SBI undef);
242    o add hooks for new packages OASIS, the package will follow
243      (hooks exclude the seaice pkg for now)
244    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
245      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
246      rather than mdsio_readvector.F/mdsio_writevector.F, within
247      adread_adwrite.F to read/write adjoint-related tapes to disk.
248    o eesupp and pkg/mdsio: ALLOW_WHIO
249      Option to write/read 2D fields to files including tiles halos.
250      The main purpose is for adjoint related "tape I/O".
251      The secondary purpose is for debugging phases.
252      A word on those rather specifically intended purposes.
253      The code was meant to be stripped down to the bare minimum.
254      Typically, there is a unique and basic mapping to the global
255      buffer (tile by tile, then proc by proc, then level by level), and
256      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
257      meant to generate user friendly outputs of various shapes and forms.
258      Rather it is intended, for the knowledgeabale developers,
259      to be largely independent of the many mdsio options, to allow
260      outputs of tiles+halos in debugging phases and in adjoint runs,
261      and to allow some flexibility in tuning (adoint) I/O depending on each
262      file system behavior. With regard to tuning, most of the potential knobs
263      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
264      to specify directories, to specify the typical size of I/O calls, etc.)
265      are not yet included, and will be added if they prove useful.
266    o pkg/seaice:
267       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
268    o pkg/seaice:
269       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
270       code (seaice_budget_ice_if.F) which enable to recover old standard
271       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
272       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
273    o model/src (rStar):
274       use simple average (not area weighted) of rStarFac at U,V point when using
275       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
276       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
277    
278    checkpoint62k (2010/09/17)
279    o adjoint
280       * changed verification/global_ocean.cs32x15 ; adjoint now tests
281         Adams-Bashforth 3 + NLFS + RSTAR
282       * some more modifs required for ECCO-GODAE v4
283    o pkg/seaice
284       add SEAICE_AGE_VOL option to use volume instead of area for
285       integrating SEAICE_AGE
286    o model/src:
287       first check-in of sigma & hybrid-sigma coordinate code ; also includes
288       non-linear free-surface parts ; but pressure-gradient not yet coded.
289    o pkg/ptracers:
290       option for ptracer to convert Salt Relax into additional EmP.
291        tested in exp. global_ocean.90x40x15.dwnslp (update output)
292    
293    checkpoint62j (2010/08/25)
294    o pkg/ggl90:
295       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
296    o pkg/dic: car_flux.F, phos_flux.F
297      - reduce number of exp-calls in order to improve performance
298      - clean up a little (replace fields by their macros, etc., fix
299        typo in CPP-flag)
300    o pkg/ggl90: minor changes
301      - GGL90diffKrS was removed --> always use GGL90diffKr
302      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
303      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
304        (commented out for now)
305      - change in max/min operations to ensure that smoothing is ok
306      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
307      - always use diffKrNrT as background profile (i.e. never use diffKr field)
308    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
309    o pkg/dic:
310      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
311        vectorization
312      - small bug fix in insol for the unlikely case of a cartesian grid
313      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
314        + now vectorize, which also removes adjoint recomputations;
315        + replace integer maksp1 by _RL maskp1
316        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
317    
318    checkpoint62i (2010/07/21)
319    o pkg/flt:
320      - with OBCS: stop floats which enter the OB region
321    o model/src:
322      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
323        for implicit vertical advection.
324    o pkg/seaice:
325     - account for melting in seaice age evolution.
326     - remove double counting of seaice ridging effect on seaice age.
327    
328    checkpoint62h (2010/06/18)
329  o pkg/exch2:  o pkg/exch2:
330   - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).   - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
331  o tools/genmake2  o tools/genmake2
# Line 230  o tools/build_options: Line 552  o tools/build_options:
552      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
553  o pkg/ecco  o pkg/ecco
554    - allow user defined cost function contributions    - allow user defined cost function contributions
555          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
556          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
557    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
558        the two options are complementary.        the two options are complementary.
559  o pkg/smooth  o pkg/smooth

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