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revision 1.1823 by jmc, Tue Feb 12 22:26:11 2013 UTC revision 1.1887 by jmc, Fri Jun 28 21:26:17 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/atm_phys:
8      - allows to add some damping on uVel,vVel (strength only function of k).
9    o verification, ad-tests:
10      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
11        global_ocean_ebm and offline_exf_seaice.thsice.
12    o verification/halfpipe_streamice:
13      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
14        flux input boundary conditions to be ignored; a fix for this bug changed
15        verification results for forward test.
16      - add adjoint test.
17    o pkg/ptracers:
18      - allow to restart without SOM pickup (resetting SOM to zero).
19    o pkg/gmredi:
20      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
21      - It uses mixing length theory and suppression by steering level effects to
22        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
23        to JPO, for more details).
24      - It also uses the diffusivity to calculate an eddy induced streamfunction
25        based on a PV closure (rather than a buoyancy closure as in GM).
26      - New files added to pkg/gmredi:
27        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
28          induced overturning streamfunction (called from gmredi_calc_tensor)
29        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
30          for use in gmredi_k3d
31        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
32          the eddy diffusivity
33    
34    checkpoint64i (2013/06/18)
35    o pkg/cheapaml:
36      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
37        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
38        with pkg/cheapaml.
39    o utils/python: add subpackage for cubed sphere function, first example is
40        simple cs.pcol to plot 2D fields on a map
41    o pkg/streamice:
42      - This is a new package in MITgcm, which solves dynamic equations for ice
43         sheets and ice streams
44      - At the moment it is independent of atmosphere/ocean dynamics, or any
45        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
46        ed that this will change)
47      - There is a new verification exercise that tests it, halfpipe_streamice,
48        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
49        rectangular embayment
50      - halfpipe_streamice is forward-only for now, will have TAF test soon
51      - for questions, email dgoldber@mit.edu
52    o pkg/thsice:
53      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
54        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
55      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
56         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
57      - allow precip from pkg/cheapaml to make snow over seaice.
58    o pkg/cfc:
59      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
60      - remove atmos CFC 2-D arrays from common bloc (now local variables)
61      - change some hard-coded constant to run time parameter for reading and
62        and interpolating atmospheric CFC ; keep same default as previously.
63      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
64      - put arguments in standard order: myTime, myIter, myThid
65      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
66        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
67      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
68      - new routine to print summary of CFC params and check for consistency.
69    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
70      similar to thsice_advdiff.
71      Note that for the B-grid case the routine parameters uc/vc are overwritten.
72    o pkg/cfc:
73      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
74        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
75      - fix interpolation of atmphspheric CFC between Sorthern and Northern
76        hemisphere value.
77    o pkg/seaice:
78      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
79    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
80                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
81      - requires an additional time level that is stored in the pickup
82      - you can start with AB2 from a pickup without this time level with
83        pickupStrictlyMatch = .false.
84    
85    checkpoint64h (2013/05/26)
86    o pkg/cheapaml:
87      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
88        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
89      - consistent treatment of uWind,vWind location: assume everywhere in
90        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
91        (Note: was already the case for Tair,Qair advection);
92        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
93      - compute diabatic forcing only in the interior (excluding overlap regions)
94      - fill in array "Qsw" (for short-wave heating);
95      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
96        before any update (consistent with MITgcm state var diagnostics);
97      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
98        non periodic ; + adjusted for uWind,vWind (C-grid).
99    o pkg/seaice:
100      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
101        add explicitly pkg/exf in experiments that currently use pkg/seaice.
102      - allows to compile pkg/seaice without pkg/exf.
103    o tools/OAD_support:
104      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
105        of array "ourStepOf" in function rvNextAction (revolve.F90).
106    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
107      - change pkg name (to be used with other atmospheric physics pkg)
108        but by-pass CVS when making the new pkg so that we keep the CVS history.
109    o pkg/offline:
110      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
111        (previously called from pkg/dic_surfforcing_init.F)
112    o model/src:
113      - re-order sequence of calls within packages_init_variables.F, using
114        standard order, except for:
115         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
116         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
117    o new pkg: atm_phys
118      - add entry point and source code (previously in contrib
119          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
120        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
121      - re-order sequence of calls within packages_readparms.F,
122         packages_init_fixed.F and packages_write_pickup.F
123        (but skip packages_init_variables.F because of TAF issues).
124      - update contrib/*/atm_gray/ experiment.
125    o pkg/seaice (ITD code):
126      - simplify and fix the writing of pickup-files for ITD case
127    o pkg/seaice (ITD code):
128      - introduce floe size dependent lateral melt for ITD case;
129      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
130      - update seaice_itd experiment main output.
131    o pkg/thsice:
132      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
133        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
134        changed accordingly pkg/atm2d.
135    
136    checkpoint64g (2013/05/01)
137    o pkg/exf ALLOW_RUNOFTEMP
138      - if defined,  river and glacier runoff temperature can be read-in from
139        runoftempfile; runoftempfile needs to have same format as runofffile
140    o pkg/thsice (& pkg/bulk_force):
141      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
142        for energy content of Precip + RunOff & Evap (like with pkg/exf).
143      - change computation domain to always be the interior (without overlap).
144      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
145    o verification/tutorial_global_oce_biogeo:
146      - add preliminary OpenAD setup (still has problems)
147    o pkg/seaice:
148      - turn some parameters for choosing the convergence criterion of
149        the inexact Newton method (JFNK) into runtime parameters for convenience
150      - clean up seaice_calc_viscosities.F: remove/retire two options for
151        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
152        the results of lab_sea/input because a division has been replaced by
153        a multiplication with the reciprocal (sumNorm)
154      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
155        convergence of solver (changes results, of course), and to test some
156        new features
157    o model/src:
158      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
159      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
160      - move forcing adjustment (balancing surface forcing) in specific S/R
161        where might also be applied exchanges (if needed) to forcing arrays.
162    o pkg/shelfice:
163      - allow to specify the Ice-Shelf mass per unit area (instead of
164        shelficeLoadAnomaly) and do the conversion from one to the other
165      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
166        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
167        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
168        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
169      - update isomip experiment forward output (get machine truncation error
170        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
171    o verification/offline_exf_seaice:
172      revise data.seaice in input.thermo and input_ad and update results accordingly
173        HO = 0.2, SEAICE_areaLossFormula = 2,
174        SEAICE_growMeltByConv = .TRUE.,
175        SEAICE_doOpenWaterMelt = .TRUE.,
176      Improve consistency with input.thsice and fix the spurious 500m ice corners
177    o verification/global_ocean.cs32x15:
178      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
179        in icedyn (thsice+seaice-dyn) test and update output.
180    o verification/offline_exf_seaice:
181      - adjust list of tested variables (with testreport) and update
182        standard test output with better slection of monitored fields.
183    o pkg/cd_code:
184      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
185        experiment lab_sea.hb87
186    o tools/genmake2:
187      - change default makedepend from the system default to tools/xmakedepend:
188        When no makedepend is specified, select tools/xmakedepend it the test pass,
189        otherwise select the system default (if exist and pass the test) or
190        try to build cyrus-makedepend ; stop if none of the 3 works.
191    o pkg/exf & pkg/thsice:
192      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
193        for energy content of Precip + RunOff & Evap. Assumes:
194       1) Rain has same temp as Air.
195       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
196       3) Run-Off comes at the temp of surface water (with same Cp)
197       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
198        put directly into Latent Heat flux & should use water-vapor heat capacity.
199       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
200        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
201    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
202        (compile when SEAICE_ALLOW_JFNK is defined)
203    o pkg/thsice:
204      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
205        implementation): move THSICE_AVE call after the advection (called directly
206        from thsice_do_advect.F).
207    o verification/global_ocean.90x40x15 and OpenAD:
208      New experiment for OpenAD is identical to the one in input_ad except that
209        multiDimAdvection=.FALSE.,
210      There is still an issue with this.
211    o pkg/thsice:
212      - account for ice velocity (ocean relative velocity) in turbulent heat flux
213        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
214        and offline_exf_seaice (main test).
215    
216    checkpoint64f (2013/03/31)
217    o verification/OpenAD:
218      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
219    o verification/isomip, pkg/shelfice and OpenAD:
220      - add OpenAD setup to this exp and make shelfice package work with OpenAD
221    o verification/tutorial_global_oce_biogeo:
222      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
223    o verification/offline_exf_seaice:
224      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
225    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
226      - add OpenAD setup to this exp and make ptracers package work with OpenAD
227    o pkg/seaice/seaice_evp.F:
228       mask the asymmetric contribution of the ice-ocean stress (when
229       the turningAngle is non-zero) over open water to avoid stripes
230       in the EVP-solutions after many EVP-substeps. This does not change
231       the verification experiment (because turningAngle=0 in that experiment),
232       but will affect other EVP solutions with turningAngle.ne.0
233    o verification, AD & TLM output:
234      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
235        additions and multiplications which affect results at machine truncation
236        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
237        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
238        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
239        digits of matching.
240    o pkg/seaice:
241       modify lsr-algorithm so that it vectorizes AND converges by using a
242       "zebra" method: split vector loop into two with step size 2; this
243       solves a general convergence problem for the JFNK solver on a vector
244       computer. It has the potential to even improve convergence for
245       non-vector machines, but it does change the results so it is turned
246       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
247       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
248    
249    checkpoint64e (2013/03/05)
250    o pkg/ecco and several verification experiments:
251       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
252       from ecco package, and revert to unified routine in model/src/
253       Adjust verification experiments accordingly, especially gloal_oce_llc90
254       Should conclude long-standing work by Gael to reconsile the_main_loop with
255       ECCO and will enable OpenAD's revolve loop in ECCO setup.
256    o pkg/generic_advdiff:
257      - implement compressible flow method for multi-dim advection (similar to
258        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
259        TAF generates many recomputations) to use it; no yet coded with implicit
260        vertical advection.
261      - change experiment advect_cs (new output) and advect_xy (same output)
262        to test compressible flow multi-dim advection.
263    o pkg/generic_advdiff:
264      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
265        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
266    o pkg/seaice:
267      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
268        bug affects two verification experiments (lab_sea and lab_sea.hb87),
269        recover old (wrong) results by setting noSlipFac = 2. in
270        seaice_calc_strainrates.F;
271      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
272      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
273        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
274      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
275    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
276      - new subroutines seaice_lsr_tridiagu/v
277      - introduce loop bounds i/jmin/max to be able to use a restricted
278        additive Schwarz method, but not used for now.
279      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
280      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
281    o OpenAD support
282       Reorganize S/R call for overall time-stepping loop to facilitate
283       OpenAD revolve loop replacement
284       (new S/R main_do_loop.F)
285    o model/src:
286      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
287      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
288        ADAMS_BASHFORTH2.
289    o pkg/cheapaml:
290      - add new parameter (default=F, same as before) to disable full domain
291        (including land) periodicity in X & Y dir.
292      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
293        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
294        into single S/R CHEAPAML_TIMESTEP.
295    
296    checkpoint64d (2013/02/17)
297    o pkg/monitor (angular momentum):
298      - do not add Eta contribution to the total AM if using rigid-lid;
299      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
300      - horizontal discretisation: compute Zonal wind contribution separately for
301        each component (instead of from cell centered averaged) and use the 4
302        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
303      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
304        FreeSurf) if using vectorInvariant momentum.
305    o model/src (horizontal grid):
306      - move initialisation of all horizontal grid arrays to null value
307        from specific horizontal grid S/R to main S/R INI_GRID;
308      - add 2 new arrays to project model C-grid velocity on to zonal direction
309        (similar to AngleCosC & -AngleSinC but at U and V point location) and
310        compute them in S/R CALC_GRID_ANGLES.
311    o pkg/seaice: replace a hard coded parameter by a runtime parameter
312        SEAICE_JFNK_tolIter
313    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
314        preconditioner for JFNK (run LSR into the overlaps as far as possible,
315        i.e OLx/y-2, but overwrite the solution in the overlaps)
316      - extend loop range in seaice_calc_viscosity
317      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
318      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
319      - slightly modify loops in tridiagonal solver lsr-preconditioner
320      - by default remove the extra exchange in seaice_preconditioner with a
321        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
322      - modify offline_exf_seaice so that old results without RAS are reproduced
323        for output.dyn_jfnk.txt
324      in seaice_fgmres.F (unrelated to RAS)
325      - add a cpp-flag option for a re-ordered mapping (potentially more
326        efficient), but because this changes the results, turn it off by
327        default
328      - replace the save statement by local common blocks
329  o utils/matlab:  o utils/matlab:
330    - fix tile-offset in rdmnc.m when output was produced using EXCH2.    - fix tile-offset in rdmnc.m when output was produced using EXCH2.
331    - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)    - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)

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