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revision 1.1865 by jmc, Wed May 8 00:08:31 2013 UTC revision 1.1928 by jmc, Sun Oct 6 00:48:15 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 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    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    checkpoint64o (2013/09/25)
21    o pkg/atm_phys & atm_compon_interf:
22      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
23    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    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      - fixed up the calculation of the eddy stress and how it is added to the
30        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    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    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    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      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
45        update accordingly + simplify aim_do_physics.F
46    
47    checkpoint64n (2013/08/26)
48    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    o verification/halfpipe_streamice:
53      - change to matrix construction; update both Fwd & AD output.
54    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    o tools:
58      - 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    o pkg/offline:
62      - changes for use with rStar (NLFS): assume that we continue to provide
63        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    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    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    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    checkpoint64m (2013/08/13)
91    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    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      - 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    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    checkpoint64l (2013/08/05)
120    o model/src:
121      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
122      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
123        when using TAF but only if using OpenAD.
124    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    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    o model/src:
146      - extend length of drC & recip_drC from Nr to Nr+1.
147    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    checkpoint64k (2013/07/23)
153    o tools/OAD_support:
154      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
155        and remove it from genmake2.
156    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    o verification/halfpipe_streamice:
160      - 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    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    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    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      - comment out resetting of monitorFreq (to endTime) since it still useful
186        for monitoring CFL numbers and checking offline fields.
187    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    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    checkpoint64j (2013/07/04)
207    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    o pkg/exf ALLOW_RUNOFTEMP
212      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
213      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
214      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
215    o pkg/atm_phys:
216      - allows to add some damping on uVel,vVel (strength only function of k).
217    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    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        verification results for forward test.
224      - add adjoint test.
225    o pkg/ptracers:
226      - allow to restart without SOM pickup (resetting SOM to zero).
227    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      - New files added to pkg/gmredi:
235        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    
242    checkpoint64i (2013/06/18)
243    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    o pkg/streamice:
250      - This is a new package in MITgcm, which solves dynamic equations for ice
251         sheets and ice streams
252      - At the moment it is independent of atmosphere/ocean dynamics, or any
253        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
254        ed that this will change)
255      - There is a new verification exercise that tests it, halfpipe_streamice,
256        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    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    o pkg/cfc:
267      - 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    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    o pkg/cfc:
281      - 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      - fix interpolation of atmphspheric CFC between Sorthern and Northern
284        hemisphere value.
285    o pkg/seaice:
286      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
287    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    checkpoint64h (2013/05/26)
294    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    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    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    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  o new pkg: atm_phys  o new pkg: atm_phys
326    - add entry point for new pkg "atm_phys" (atmospheric physics pkg    - add entry point and source code (previously in contrib
327      from P. O'Gorman and T. Schneider, JCl, 2008).        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    - re-order sequence of calls within packages_readparms.F,    - re-order sequence of calls within packages_readparms.F,
330       packages_init_fixed.F and packages_write_pickup.F       packages_init_fixed.F and packages_write_pickup.F
331      (but skip packages_init_variables.F because of TAF issues).      (but skip packages_init_variables.F because of TAF issues).
332      - update contrib/*/atm_gray/ experiment.
333  o pkg/seaice (ITD code):  o pkg/seaice (ITD code):
334    - simplify and fix the writing of pickup-files for ITD case    - simplify and fix the writing of pickup-files for ITD case
335  o pkg/seaice (ITD code):  o pkg/seaice (ITD code):

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