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revision 1.1827 by jmc, Sun Feb 17 23:10:07 2013 UTC revision 1.1894 by jmc, Sun Jul 7 22:28:10 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/offline:
8      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
9      - add S/R OFFLINE_CHECK to print offline parameter summary
10        and stop if loading a file that is not used;
11      - enable to calculate GMRedi tensor, KPP mixing and convective index
12        when the corresponding file(s) is/are not specified (but pkg is used).
13    o OpenAD:
14      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
15        smaller standard output) and generate new (smaller) output (on baudelaire
16        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
17    o model/src:
18      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
19        (where external_forcing_adjust was called) and change list of arguments;
20      - merge external_forcing_adjust.F into external_forcing_surf.F
21      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
22        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
23        previously in file "balance_relax.F", now removed); remove corresponding
24        arrays in FFIELDS.h.
25      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
26        a hack for getting back surfaceForcingS (loaded from file) when using
27        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
28      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
29        (was getting only 11 digits for AD-grad, due to different truncation
30         error in AD code).
31    
32    checkpoint64j (2013/07/04)
33    o pkg/offline:
34      - to enable the use of other features with pkg offline (e.g., obcs),
35        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
36      - comment out "allowFreezing" (now active) in 2 offline testing exp.
37    o pkg/exf ALLOW_RUNOFTEMP
38      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
39      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
40      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
41    o pkg/atm_phys:
42      - allows to add some damping on uVel,vVel (strength only function of k).
43    o verification, ad-tests:
44      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
45        global_ocean_ebm and offline_exf_seaice.thsice.
46    o verification/halfpipe_streamice:
47      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
48        flux input boundary conditions to be ignored; a fix for this bug changed
49        verification results for forward test.
50      - add adjoint test.
51    o pkg/ptracers:
52      - allow to restart without SOM pickup (resetting SOM to zero).
53    o pkg/gmredi:
54      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
55      - It uses mixing length theory and suppression by steering level effects to
56        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
57        to JPO, for more details).
58      - It also uses the diffusivity to calculate an eddy induced streamfunction
59        based on a PV closure (rather than a buoyancy closure as in GM).
60      - New files added to pkg/gmredi:
61        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
62          induced overturning streamfunction (called from gmredi_calc_tensor)
63        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
64          for use in gmredi_k3d
65        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
66          the eddy diffusivity
67    
68    checkpoint64i (2013/06/18)
69    o pkg/cheapaml:
70      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
71        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
72        with pkg/cheapaml.
73    o utils/python: add subpackage for cubed sphere function, first example is
74        simple cs.pcol to plot 2D fields on a map
75    o pkg/streamice:
76      - This is a new package in MITgcm, which solves dynamic equations for ice
77         sheets and ice streams
78      - At the moment it is independent of atmosphere/ocean dynamics, or any
79        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
80        ed that this will change)
81      - There is a new verification exercise that tests it, halfpipe_streamice,
82        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
83        rectangular embayment
84      - halfpipe_streamice is forward-only for now, will have TAF test soon
85      - for questions, email dgoldber@mit.edu
86    o pkg/thsice:
87      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
88        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
89      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
90         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
91      - allow precip from pkg/cheapaml to make snow over seaice.
92    o pkg/cfc:
93      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
94      - remove atmos CFC 2-D arrays from common bloc (now local variables)
95      - change some hard-coded constant to run time parameter for reading and
96        and interpolating atmospheric CFC ; keep same default as previously.
97      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
98      - put arguments in standard order: myTime, myIter, myThid
99      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
100        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
101      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
102      - new routine to print summary of CFC params and check for consistency.
103    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
104      similar to thsice_advdiff.
105      Note that for the B-grid case the routine parameters uc/vc are overwritten.
106    o pkg/cfc:
107      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
108        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
109      - fix interpolation of atmphspheric CFC between Sorthern and Northern
110        hemisphere value.
111    o pkg/seaice:
112      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
113    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
114                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
115      - requires an additional time level that is stored in the pickup
116      - you can start with AB2 from a pickup without this time level with
117        pickupStrictlyMatch = .false.
118    
119    checkpoint64h (2013/05/26)
120    o pkg/cheapaml:
121      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
122        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
123      - consistent treatment of uWind,vWind location: assume everywhere in
124        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
125        (Note: was already the case for Tair,Qair advection);
126        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
127      - compute diabatic forcing only in the interior (excluding overlap regions)
128      - fill in array "Qsw" (for short-wave heating);
129      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
130        before any update (consistent with MITgcm state var diagnostics);
131      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
132        non periodic ; + adjusted for uWind,vWind (C-grid).
133    o pkg/seaice:
134      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
135        add explicitly pkg/exf in experiments that currently use pkg/seaice.
136      - allows to compile pkg/seaice without pkg/exf.
137    o tools/OAD_support:
138      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
139        of array "ourStepOf" in function rvNextAction (revolve.F90).
140    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
141      - change pkg name (to be used with other atmospheric physics pkg)
142        but by-pass CVS when making the new pkg so that we keep the CVS history.
143    o pkg/offline:
144      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
145        (previously called from pkg/dic_surfforcing_init.F)
146    o model/src:
147      - re-order sequence of calls within packages_init_variables.F, using
148        standard order, except for:
149         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
150         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
151    o new pkg: atm_phys
152      - add entry point and source code (previously in contrib
153          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
154        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
155      - re-order sequence of calls within packages_readparms.F,
156         packages_init_fixed.F and packages_write_pickup.F
157        (but skip packages_init_variables.F because of TAF issues).
158      - update contrib/*/atm_gray/ experiment.
159    o pkg/seaice (ITD code):
160      - simplify and fix the writing of pickup-files for ITD case
161    o pkg/seaice (ITD code):
162      - introduce floe size dependent lateral melt for ITD case;
163      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
164      - update seaice_itd experiment main output.
165    o pkg/thsice:
166      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
167        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
168        changed accordingly pkg/atm2d.
169    
170    checkpoint64g (2013/05/01)
171    o pkg/exf ALLOW_RUNOFTEMP
172      - if defined,  river and glacier runoff temperature can be read-in from
173        runoftempfile; runoftempfile needs to have same format as runofffile
174    o pkg/thsice (& pkg/bulk_force):
175      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
176        for energy content of Precip + RunOff & Evap (like with pkg/exf).
177      - change computation domain to always be the interior (without overlap).
178      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
179    o verification/tutorial_global_oce_biogeo:
180      - add preliminary OpenAD setup (still has problems)
181    o pkg/seaice:
182      - turn some parameters for choosing the convergence criterion of
183        the inexact Newton method (JFNK) into runtime parameters for convenience
184      - clean up seaice_calc_viscosities.F: remove/retire two options for
185        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
186        the results of lab_sea/input because a division has been replaced by
187        a multiplication with the reciprocal (sumNorm)
188      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
189        convergence of solver (changes results, of course), and to test some
190        new features
191    o model/src:
192      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
193      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
194      - move forcing adjustment (balancing surface forcing) in specific S/R
195        where might also be applied exchanges (if needed) to forcing arrays.
196    o pkg/shelfice:
197      - allow to specify the Ice-Shelf mass per unit area (instead of
198        shelficeLoadAnomaly) and do the conversion from one to the other
199      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
200        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
201        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
202        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
203      - update isomip experiment forward output (get machine truncation error
204        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
205    o verification/offline_exf_seaice:
206      revise data.seaice in input.thermo and input_ad and update results accordingly
207        HO = 0.2, SEAICE_areaLossFormula = 2,
208        SEAICE_growMeltByConv = .TRUE.,
209        SEAICE_doOpenWaterMelt = .TRUE.,
210      Improve consistency with input.thsice and fix the spurious 500m ice corners
211    o verification/global_ocean.cs32x15:
212      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
213        in icedyn (thsice+seaice-dyn) test and update output.
214    o verification/offline_exf_seaice:
215      - adjust list of tested variables (with testreport) and update
216        standard test output with better slection of monitored fields.
217    o pkg/cd_code:
218      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
219        experiment lab_sea.hb87
220    o tools/genmake2:
221      - change default makedepend from the system default to tools/xmakedepend:
222        When no makedepend is specified, select tools/xmakedepend it the test pass,
223        otherwise select the system default (if exist and pass the test) or
224        try to build cyrus-makedepend ; stop if none of the 3 works.
225    o pkg/exf & pkg/thsice:
226      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
227        for energy content of Precip + RunOff & Evap. Assumes:
228       1) Rain has same temp as Air.
229       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
230       3) Run-Off comes at the temp of surface water (with same Cp)
231       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
232        put directly into Latent Heat flux & should use water-vapor heat capacity.
233       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
234        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
235    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
236        (compile when SEAICE_ALLOW_JFNK is defined)
237    o pkg/thsice:
238      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
239        implementation): move THSICE_AVE call after the advection (called directly
240        from thsice_do_advect.F).
241    o verification/global_ocean.90x40x15 and OpenAD:
242      New experiment for OpenAD is identical to the one in input_ad except that
243        multiDimAdvection=.FALSE.,
244      There is still an issue with this.
245    o pkg/thsice:
246      - account for ice velocity (ocean relative velocity) in turbulent heat flux
247        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
248        and offline_exf_seaice (main test).
249    
250    checkpoint64f (2013/03/31)
251    o verification/OpenAD:
252      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
253    o verification/isomip, pkg/shelfice and OpenAD:
254      - add OpenAD setup to this exp and make shelfice package work with OpenAD
255    o verification/tutorial_global_oce_biogeo:
256      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
257    o verification/offline_exf_seaice:
258      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
259    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
260      - add OpenAD setup to this exp and make ptracers package work with OpenAD
261    o pkg/seaice/seaice_evp.F:
262       mask the asymmetric contribution of the ice-ocean stress (when
263       the turningAngle is non-zero) over open water to avoid stripes
264       in the EVP-solutions after many EVP-substeps. This does not change
265       the verification experiment (because turningAngle=0 in that experiment),
266       but will affect other EVP solutions with turningAngle.ne.0
267    o verification, AD & TLM output:
268      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
269        additions and multiplications which affect results at machine truncation
270        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
271        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
272        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
273        digits of matching.
274    o pkg/seaice:
275       modify lsr-algorithm so that it vectorizes AND converges by using a
276       "zebra" method: split vector loop into two with step size 2; this
277       solves a general convergence problem for the JFNK solver on a vector
278       computer. It has the potential to even improve convergence for
279       non-vector machines, but it does change the results so it is turned
280       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
281       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
282    
283    checkpoint64e (2013/03/05)
284    o pkg/ecco and several verification experiments:
285       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
286       from ecco package, and revert to unified routine in model/src/
287       Adjust verification experiments accordingly, especially gloal_oce_llc90
288       Should conclude long-standing work by Gael to reconsile the_main_loop with
289       ECCO and will enable OpenAD's revolve loop in ECCO setup.
290    o pkg/generic_advdiff:
291      - implement compressible flow method for multi-dim advection (similar to
292        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
293        TAF generates many recomputations) to use it; no yet coded with implicit
294        vertical advection.
295      - change experiment advect_cs (new output) and advect_xy (same output)
296        to test compressible flow multi-dim advection.
297    o pkg/generic_advdiff:
298      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
299        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
300    o pkg/seaice:
301      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
302        bug affects two verification experiments (lab_sea and lab_sea.hb87),
303        recover old (wrong) results by setting noSlipFac = 2. in
304        seaice_calc_strainrates.F;
305      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
306      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
307        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
308      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
309    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
310      - new subroutines seaice_lsr_tridiagu/v
311      - introduce loop bounds i/jmin/max to be able to use a restricted
312        additive Schwarz method, but not used for now.
313      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
314      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
315    o OpenAD support
316       Reorganize S/R call for overall time-stepping loop to facilitate
317       OpenAD revolve loop replacement
318       (new S/R main_do_loop.F)
319    o model/src:
320      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
321      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
322        ADAMS_BASHFORTH2.
323    o pkg/cheapaml:
324      - add new parameter (default=F, same as before) to disable full domain
325        (including land) periodicity in X & Y dir.
326      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
327        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
328        into single S/R CHEAPAML_TIMESTEP.
329    
330  checkpoint64d (2013/02/17)  checkpoint64d (2013/02/17)
331  o pkg/monitor (angular momentum):  o pkg/monitor (angular momentum):
332    - do not add Eta contribution to the total AM if using rigid-lid;    - do not add Eta contribution to the total AM if using rigid-lid;

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