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revision 1.1851 by jmc, Fri Apr 5 21:29:21 2013 UTC revision 1.1914 by jahn, Wed Aug 21 00:25:30 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o adjoint with OpenAD:
8      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
9        package openad.  This package has to be compiled for all runs with OpenAD
10        instead of specifying code_oad_all as a modification directory.
11      - link the fortran templates from tools/OAD_support to the build directory
12        for preprocessing to avoid conflicts between different setups compiled
13        simultaneously and simplify cleanup.
14    o pkg/exf:
15      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
16        main model or other pkgs are exchanged in EXF_MAPFIELDS).
17    o model/src:
18      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
19        (similar to do_fields_blocking_exchanges.F).
20    o tools/genmake2:
21      - remove TAF output src code just before calling staf (when not doing a fresh
22        built, will stop if things go wrong with staf).
23      - fix target "adobj" (left from TAF version-2 transition)
24    o pkg/diagnostics:
25      - add a parameter to track the status of pkg/diagnostics activation;
26        this replace/extend the use of logical param "settingDiags" (to check
27        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
28        New S/R to print error message and stop when pkgStatus is not right.
29      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
30    
31    checkpoint64m (2013/08/13)
32    o model/inc:
33      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
34        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
35    o pkg/kpp & aim_v23:
36      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
37    o pkg/seaice:
38      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
39        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
40      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
41    o eesupp/src:
42      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
43        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
44    o switch to TAF version-2:
45      - add flow directives to "freeze" naming convention for ad-routines that
46        are used in I/O routines of adjoint state and associated common blocks
47        that are used in adcommon.h (backward compatible with version-1)
48      - update all ad-optfiles (in tools/adjoint_options + few local to some
49        verification exp) to switch to latest TAF version (currently 2.5.5);
50        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
51        out except for diva).
52      - the major change with TAF version-2 is that both the differentiated
53        routines and the forward routines (new) are returned as part of the TAF
54        output source code. Update genmake2 accordingly.
55      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
56        with version-2 when compared to TLM or FWD gradient); other experiments
57        output show minor changes (machine truncation level); update the few AD &
58        TLM output with 12 matching digits only (some prior to version-2 switch).
59    
60    checkpoint64l (2013/08/05)
61    o model/src:
62      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
63      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
64        when using TAF but only if using OpenAD.
65    o pkg/mom_common+fluxform+vecinv:
66      - always set horiz. viscosity arrays to background value before calling
67        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
68        only when using variable horiz. viscosity (useVariableVisc=T);
69      - simplify mom_vecinv.F (only 1 block for momViscosity).
70    o pkg/mom_common: variable horiz. viscosity in NH code
71      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
72        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
73      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
74        useBiharmonicVisc & useVariableVisc.
75      - fix old bug (already in 1rst implementation of variable horizontal viscosity
76        in calc_gw.F, version 1.27, 2006/06/20):
77        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
78        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
79      - change background horiz viscosity in vertical momentum (gW) to always be
80        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
81        any type of variable viscosity, e.g., viscAh/4Grid)
82      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
83        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
84        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
85        default viscAh,viscA4 is zero).
86    o model/src:
87      - extend length of drC & recip_drC from Nr to Nr+1.
88    o Divided Adjoint (DIVA) with MPI:
89      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
90      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
91        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
92    
93    checkpoint64k (2013/07/23)
94    o tools/OAD_support:
95      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
96        and remove it from genmake2.
97    o tools/build_options:
98      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
99        MPI_HEADER_FILES list (let genmake2 find the missing headers)
100    o verification/halfpipe_streamice:
101      - change to driving stress formulation; update both Fwd & AD output.
102    o tools/genmake2 and Divided Adjoint with MPI:
103      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
104      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
105      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
106        Makefile, which is set by genmake2, and check which mpi-headers are needed.
107        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
108      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
109    o testreport:
110      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
111        perform additional runs (number of additional runs is "add_DIVA_runs" taken
112        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
113    o verification/lab_sea (AD test):
114      - change to test Divided Adjoint Run in this set-up (both standard AD test
115        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
116    o pkg atm_ & ocn_compon_interf:
117      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
118        staggerTimeStep implementation) and disable (retired) corresponding
119        parameter.
120    o pkg/offline:
121      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
122      - add S/R OFFLINE_CHECK to print offline parameter summary
123        and stop if loading a file that is not used;
124      - enable to calculate GMRedi tensor, KPP mixing and convective index
125        when the corresponding file(s) is/are not specified (but pkg is used).
126      - comment out resetting of monitorFreq (to endTime) since it still useful
127        for monitoring CFL numbers and checking offline fields.
128    o OpenAD:
129      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
130        smaller standard output) and generate new (smaller) output (on baudelaire
131        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
132    o model/src:
133      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
134        (where external_forcing_adjust was called) and change list of arguments;
135      - merge external_forcing_adjust.F into external_forcing_surf.F
136      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
137        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
138        previously in file "balance_relax.F", now removed); remove corresponding
139        arrays in FFIELDS.h.
140      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
141        a hack for getting back surfaceForcingS (loaded from file) when using
142        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
143      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
144        (was getting only 11 digits for AD-grad, due to different truncation
145         error in AD code).
146    
147    checkpoint64j (2013/07/04)
148    o pkg/offline:
149      - to enable the use of other features with pkg offline (e.g., obcs),
150        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
151      - comment out "allowFreezing" (now active) in 2 offline testing exp.
152    o pkg/exf ALLOW_RUNOFTEMP
153      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
154      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
155      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
156    o pkg/atm_phys:
157      - allows to add some damping on uVel,vVel (strength only function of k).
158    o verification, ad-tests:
159      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
160        global_ocean_ebm and offline_exf_seaice.thsice.
161    o verification/halfpipe_streamice:
162      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
163        flux input boundary conditions to be ignored; a fix for this bug changed
164        verification results for forward test.
165      - add adjoint test.
166    o pkg/ptracers:
167      - allow to restart without SOM pickup (resetting SOM to zero).
168    o pkg/gmredi:
169      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
170      - It uses mixing length theory and suppression by steering level effects to
171        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
172        to JPO, for more details).
173      - It also uses the diffusivity to calculate an eddy induced streamfunction
174        based on a PV closure (rather than a buoyancy closure as in GM).
175      - New files added to pkg/gmredi:
176        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
177          induced overturning streamfunction (called from gmredi_calc_tensor)
178        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
179          for use in gmredi_k3d
180        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
181          the eddy diffusivity
182    
183    checkpoint64i (2013/06/18)
184    o pkg/cheapaml:
185      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
186        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
187        with pkg/cheapaml.
188    o utils/python: add subpackage for cubed sphere function, first example is
189        simple cs.pcol to plot 2D fields on a map
190    o pkg/streamice:
191      - This is a new package in MITgcm, which solves dynamic equations for ice
192         sheets and ice streams
193      - At the moment it is independent of atmosphere/ocean dynamics, or any
194        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
195        ed that this will change)
196      - There is a new verification exercise that tests it, halfpipe_streamice,
197        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
198        rectangular embayment
199      - halfpipe_streamice is forward-only for now, will have TAF test soon
200      - for questions, email dgoldber@mit.edu
201    o pkg/thsice:
202      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
203        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
204      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
205         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
206      - allow precip from pkg/cheapaml to make snow over seaice.
207    o pkg/cfc:
208      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
209      - remove atmos CFC 2-D arrays from common bloc (now local variables)
210      - change some hard-coded constant to run time parameter for reading and
211        and interpolating atmospheric CFC ; keep same default as previously.
212      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
213      - put arguments in standard order: myTime, myIter, myThid
214      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
215        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
216      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
217      - new routine to print summary of CFC params and check for consistency.
218    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
219      similar to thsice_advdiff.
220      Note that for the B-grid case the routine parameters uc/vc are overwritten.
221    o pkg/cfc:
222      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
223        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
224      - fix interpolation of atmphspheric CFC between Sorthern and Northern
225        hemisphere value.
226    o pkg/seaice:
227      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
228    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
229                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
230      - requires an additional time level that is stored in the pickup
231      - you can start with AB2 from a pickup without this time level with
232        pickupStrictlyMatch = .false.
233    
234    checkpoint64h (2013/05/26)
235    o pkg/cheapaml:
236      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
237        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
238      - consistent treatment of uWind,vWind location: assume everywhere in
239        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
240        (Note: was already the case for Tair,Qair advection);
241        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
242      - compute diabatic forcing only in the interior (excluding overlap regions)
243      - fill in array "Qsw" (for short-wave heating);
244      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
245        before any update (consistent with MITgcm state var diagnostics);
246      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
247        non periodic ; + adjusted for uWind,vWind (C-grid).
248    o pkg/seaice:
249      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
250        add explicitly pkg/exf in experiments that currently use pkg/seaice.
251      - allows to compile pkg/seaice without pkg/exf.
252    o tools/OAD_support:
253      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
254        of array "ourStepOf" in function rvNextAction (revolve.F90).
255    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
256      - change pkg name (to be used with other atmospheric physics pkg)
257        but by-pass CVS when making the new pkg so that we keep the CVS history.
258    o pkg/offline:
259      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
260        (previously called from pkg/dic_surfforcing_init.F)
261    o model/src:
262      - re-order sequence of calls within packages_init_variables.F, using
263        standard order, except for:
264         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
265         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
266    o new pkg: atm_phys
267      - add entry point and source code (previously in contrib
268          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
269        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
270      - re-order sequence of calls within packages_readparms.F,
271         packages_init_fixed.F and packages_write_pickup.F
272        (but skip packages_init_variables.F because of TAF issues).
273      - update contrib/*/atm_gray/ experiment.
274    o pkg/seaice (ITD code):
275      - simplify and fix the writing of pickup-files for ITD case
276    o pkg/seaice (ITD code):
277      - introduce floe size dependent lateral melt for ITD case;
278      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
279      - update seaice_itd experiment main output.
280    o pkg/thsice:
281      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
282        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
283        changed accordingly pkg/atm2d.
284    
285    checkpoint64g (2013/05/01)
286    o pkg/exf ALLOW_RUNOFTEMP
287      - if defined,  river and glacier runoff temperature can be read-in from
288        runoftempfile; runoftempfile needs to have same format as runofffile
289    o pkg/thsice (& pkg/bulk_force):
290      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
291        for energy content of Precip + RunOff & Evap (like with pkg/exf).
292      - change computation domain to always be the interior (without overlap).
293      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
294    o verification/tutorial_global_oce_biogeo:
295      - add preliminary OpenAD setup (still has problems)
296    o pkg/seaice:
297      - turn some parameters for choosing the convergence criterion of
298        the inexact Newton method (JFNK) into runtime parameters for convenience
299      - clean up seaice_calc_viscosities.F: remove/retire two options for
300        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
301        the results of lab_sea/input because a division has been replaced by
302        a multiplication with the reciprocal (sumNorm)
303      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
304        convergence of solver (changes results, of course), and to test some
305        new features
306    o model/src:
307      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
308      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
309      - move forcing adjustment (balancing surface forcing) in specific S/R
310        where might also be applied exchanges (if needed) to forcing arrays.
311    o pkg/shelfice:
312      - allow to specify the Ice-Shelf mass per unit area (instead of
313        shelficeLoadAnomaly) and do the conversion from one to the other
314      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
315        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
316        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
317        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
318      - update isomip experiment forward output (get machine truncation error
319        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
320    o verification/offline_exf_seaice:
321      revise data.seaice in input.thermo and input_ad and update results accordingly
322        HO = 0.2, SEAICE_areaLossFormula = 2,
323        SEAICE_growMeltByConv = .TRUE.,
324        SEAICE_doOpenWaterMelt = .TRUE.,
325      Improve consistency with input.thsice and fix the spurious 500m ice corners
326    o verification/global_ocean.cs32x15:
327      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
328        in icedyn (thsice+seaice-dyn) test and update output.
329    o verification/offline_exf_seaice:
330      - adjust list of tested variables (with testreport) and update
331        standard test output with better slection of monitored fields.
332    o pkg/cd_code:
333      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
334        experiment lab_sea.hb87
335  o tools/genmake2:  o tools/genmake2:
336    - change default makedepend from the system default to tools/xmakedepend:    - change default makedepend from the system default to tools/xmakedepend:
337      When no makedepend is specified, select tools/xmakedepend it the test pass,      When no makedepend is specified, select tools/xmakedepend it the test pass,

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