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revision 1.1836 by jmc, Mon Mar 4 19:08:25 2013 UTC revision 1.1904 by jmc, Thu Aug 1 20:17:16 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/mom_common+fluxform+vecinv:
8      - always set horiz. viscosity arrays to background value before calling
9        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
10        only when using variable horiz. viscosity (useVariableVisc=T);
11      - simplify mom_vecinv.F (only 1 block for momViscosity).
12    o pkg/mom_common: variable horiz. viscosity in NH code
13      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
14        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
15      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
16        useBiharmonicVisc & useVariableVisc.
17      - fix old bug (already in 1rst implementation of variable horizontal viscosity
18        in calc_gw.F, version 1.27, 2006/06/20):
19        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
20        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
21      - change background horiz viscosity in vertical momentum (gW) to always be
22        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
23        any type of variable viscosity, e.g., viscAh/4Grid)
24      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
25        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
26        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
27        default viscAh,viscA4 is zero).
28    o model/src:
29      - extend length of drC & recip_drC from Nr to Nr+1.
30    o Divided Adjoint (DIVA) with MPI:
31      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
32      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
33        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
34    
35    checkpoint64k (2013/07/23)
36    o tools/OAD_support:
37      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
38        and remove it from genmake2.
39    o tools/build_options:
40      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
41        MPI_HEADER_FILES list (let genmake2 find the missing headers)
42    o verification/halfpipe_streamice:
43      - change to driving stress formulation; update both Fwd & AD output.
44    o tools/genmake2 and Divided Adjoint with MPI:
45      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
46      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
47      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
48        Makefile, which is set by genmake2, and check which mpi-headers are needed.
49        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
50      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
51    o testreport:
52      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
53        perform additional runs (number of additional runs is "add_DIVA_runs" taken
54        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
55    o verification/lab_sea (AD test):
56      - change to test Divided Adjoint Run in this set-up (both standard AD test
57        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
58    o pkg atm_ & ocn_compon_interf:
59      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
60        staggerTimeStep implementation) and disable (retired) corresponding
61        parameter.
62    o pkg/offline:
63      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
64      - add S/R OFFLINE_CHECK to print offline parameter summary
65        and stop if loading a file that is not used;
66      - enable to calculate GMRedi tensor, KPP mixing and convective index
67        when the corresponding file(s) is/are not specified (but pkg is used).
68      - comment out resetting of monitorFreq (to endTime) since it still useful
69        for monitoring CFL numbers and checking offline fields.
70    o OpenAD:
71      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
72        smaller standard output) and generate new (smaller) output (on baudelaire
73        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
74    o model/src:
75      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
76        (where external_forcing_adjust was called) and change list of arguments;
77      - merge external_forcing_adjust.F into external_forcing_surf.F
78      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
79        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
80        previously in file "balance_relax.F", now removed); remove corresponding
81        arrays in FFIELDS.h.
82      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
83        a hack for getting back surfaceForcingS (loaded from file) when using
84        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
85      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
86        (was getting only 11 digits for AD-grad, due to different truncation
87         error in AD code).
88    
89    checkpoint64j (2013/07/04)
90    o pkg/offline:
91      - to enable the use of other features with pkg offline (e.g., obcs),
92        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
93      - comment out "allowFreezing" (now active) in 2 offline testing exp.
94    o pkg/exf ALLOW_RUNOFTEMP
95      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
96      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
97      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
98    o pkg/atm_phys:
99      - allows to add some damping on uVel,vVel (strength only function of k).
100    o verification, ad-tests:
101      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
102        global_ocean_ebm and offline_exf_seaice.thsice.
103    o verification/halfpipe_streamice:
104      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
105        flux input boundary conditions to be ignored; a fix for this bug changed
106        verification results for forward test.
107      - add adjoint test.
108    o pkg/ptracers:
109      - allow to restart without SOM pickup (resetting SOM to zero).
110    o pkg/gmredi:
111      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
112      - It uses mixing length theory and suppression by steering level effects to
113        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
114        to JPO, for more details).
115      - It also uses the diffusivity to calculate an eddy induced streamfunction
116        based on a PV closure (rather than a buoyancy closure as in GM).
117      - New files added to pkg/gmredi:
118        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
119          induced overturning streamfunction (called from gmredi_calc_tensor)
120        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
121          for use in gmredi_k3d
122        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
123          the eddy diffusivity
124    
125    checkpoint64i (2013/06/18)
126    o pkg/cheapaml:
127      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
128        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
129        with pkg/cheapaml.
130    o utils/python: add subpackage for cubed sphere function, first example is
131        simple cs.pcol to plot 2D fields on a map
132    o pkg/streamice:
133      - This is a new package in MITgcm, which solves dynamic equations for ice
134         sheets and ice streams
135      - At the moment it is independent of atmosphere/ocean dynamics, or any
136        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
137        ed that this will change)
138      - There is a new verification exercise that tests it, halfpipe_streamice,
139        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
140        rectangular embayment
141      - halfpipe_streamice is forward-only for now, will have TAF test soon
142      - for questions, email dgoldber@mit.edu
143    o pkg/thsice:
144      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
145        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
146      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
147         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
148      - allow precip from pkg/cheapaml to make snow over seaice.
149    o pkg/cfc:
150      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
151      - remove atmos CFC 2-D arrays from common bloc (now local variables)
152      - change some hard-coded constant to run time parameter for reading and
153        and interpolating atmospheric CFC ; keep same default as previously.
154      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
155      - put arguments in standard order: myTime, myIter, myThid
156      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
157        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
158      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
159      - new routine to print summary of CFC params and check for consistency.
160    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
161      similar to thsice_advdiff.
162      Note that for the B-grid case the routine parameters uc/vc are overwritten.
163    o pkg/cfc:
164      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
165        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
166      - fix interpolation of atmphspheric CFC between Sorthern and Northern
167        hemisphere value.
168    o pkg/seaice:
169      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
170    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
171                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
172      - requires an additional time level that is stored in the pickup
173      - you can start with AB2 from a pickup without this time level with
174        pickupStrictlyMatch = .false.
175    
176    checkpoint64h (2013/05/26)
177    o pkg/cheapaml:
178      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
179        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
180      - consistent treatment of uWind,vWind location: assume everywhere in
181        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
182        (Note: was already the case for Tair,Qair advection);
183        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
184      - compute diabatic forcing only in the interior (excluding overlap regions)
185      - fill in array "Qsw" (for short-wave heating);
186      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
187        before any update (consistent with MITgcm state var diagnostics);
188      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
189        non periodic ; + adjusted for uWind,vWind (C-grid).
190    o pkg/seaice:
191      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
192        add explicitly pkg/exf in experiments that currently use pkg/seaice.
193      - allows to compile pkg/seaice without pkg/exf.
194    o tools/OAD_support:
195      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
196        of array "ourStepOf" in function rvNextAction (revolve.F90).
197    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
198      - change pkg name (to be used with other atmospheric physics pkg)
199        but by-pass CVS when making the new pkg so that we keep the CVS history.
200    o pkg/offline:
201      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
202        (previously called from pkg/dic_surfforcing_init.F)
203    o model/src:
204      - re-order sequence of calls within packages_init_variables.F, using
205        standard order, except for:
206         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
207         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
208    o new pkg: atm_phys
209      - add entry point and source code (previously in contrib
210          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
211        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
212      - re-order sequence of calls within packages_readparms.F,
213         packages_init_fixed.F and packages_write_pickup.F
214        (but skip packages_init_variables.F because of TAF issues).
215      - update contrib/*/atm_gray/ experiment.
216    o pkg/seaice (ITD code):
217      - simplify and fix the writing of pickup-files for ITD case
218    o pkg/seaice (ITD code):
219      - introduce floe size dependent lateral melt for ITD case;
220      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
221      - update seaice_itd experiment main output.
222    o pkg/thsice:
223      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
224        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
225        changed accordingly pkg/atm2d.
226    
227    checkpoint64g (2013/05/01)
228    o pkg/exf ALLOW_RUNOFTEMP
229      - if defined,  river and glacier runoff temperature can be read-in from
230        runoftempfile; runoftempfile needs to have same format as runofffile
231    o pkg/thsice (& pkg/bulk_force):
232      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
233        for energy content of Precip + RunOff & Evap (like with pkg/exf).
234      - change computation domain to always be the interior (without overlap).
235      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
236    o verification/tutorial_global_oce_biogeo:
237      - add preliminary OpenAD setup (still has problems)
238    o pkg/seaice:
239      - turn some parameters for choosing the convergence criterion of
240        the inexact Newton method (JFNK) into runtime parameters for convenience
241      - clean up seaice_calc_viscosities.F: remove/retire two options for
242        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
243        the results of lab_sea/input because a division has been replaced by
244        a multiplication with the reciprocal (sumNorm)
245      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
246        convergence of solver (changes results, of course), and to test some
247        new features
248    o model/src:
249      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
250      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
251      - move forcing adjustment (balancing surface forcing) in specific S/R
252        where might also be applied exchanges (if needed) to forcing arrays.
253    o pkg/shelfice:
254      - allow to specify the Ice-Shelf mass per unit area (instead of
255        shelficeLoadAnomaly) and do the conversion from one to the other
256      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
257        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
258        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
259        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
260      - update isomip experiment forward output (get machine truncation error
261        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
262    o verification/offline_exf_seaice:
263      revise data.seaice in input.thermo and input_ad and update results accordingly
264        HO = 0.2, SEAICE_areaLossFormula = 2,
265        SEAICE_growMeltByConv = .TRUE.,
266        SEAICE_doOpenWaterMelt = .TRUE.,
267      Improve consistency with input.thsice and fix the spurious 500m ice corners
268    o verification/global_ocean.cs32x15:
269      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
270        in icedyn (thsice+seaice-dyn) test and update output.
271    o verification/offline_exf_seaice:
272      - adjust list of tested variables (with testreport) and update
273        standard test output with better slection of monitored fields.
274    o pkg/cd_code:
275      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
276        experiment lab_sea.hb87
277    o tools/genmake2:
278      - change default makedepend from the system default to tools/xmakedepend:
279        When no makedepend is specified, select tools/xmakedepend it the test pass,
280        otherwise select the system default (if exist and pass the test) or
281        try to build cyrus-makedepend ; stop if none of the 3 works.
282    o pkg/exf & pkg/thsice:
283      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
284        for energy content of Precip + RunOff & Evap. Assumes:
285       1) Rain has same temp as Air.
286       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
287       3) Run-Off comes at the temp of surface water (with same Cp)
288       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
289        put directly into Latent Heat flux & should use water-vapor heat capacity.
290       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
291        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
292    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
293        (compile when SEAICE_ALLOW_JFNK is defined)
294    o pkg/thsice:
295      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
296        implementation): move THSICE_AVE call after the advection (called directly
297        from thsice_do_advect.F).
298    o verification/global_ocean.90x40x15 and OpenAD:
299      New experiment for OpenAD is identical to the one in input_ad except that
300        multiDimAdvection=.FALSE.,
301      There is still an issue with this.
302    o pkg/thsice:
303      - account for ice velocity (ocean relative velocity) in turbulent heat flux
304        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
305        and offline_exf_seaice (main test).
306    
307    checkpoint64f (2013/03/31)
308    o verification/OpenAD:
309      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
310    o verification/isomip, pkg/shelfice and OpenAD:
311      - add OpenAD setup to this exp and make shelfice package work with OpenAD
312    o verification/tutorial_global_oce_biogeo:
313      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
314    o verification/offline_exf_seaice:
315      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
316    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
317      - add OpenAD setup to this exp and make ptracers package work with OpenAD
318    o pkg/seaice/seaice_evp.F:
319       mask the asymmetric contribution of the ice-ocean stress (when
320       the turningAngle is non-zero) over open water to avoid stripes
321       in the EVP-solutions after many EVP-substeps. This does not change
322       the verification experiment (because turningAngle=0 in that experiment),
323       but will affect other EVP solutions with turningAngle.ne.0
324    o verification, AD & TLM output:
325      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
326        additions and multiplications which affect results at machine truncation
327        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
328        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
329        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
330        digits of matching.
331    o pkg/seaice:
332       modify lsr-algorithm so that it vectorizes AND converges by using a
333       "zebra" method: split vector loop into two with step size 2; this
334       solves a general convergence problem for the JFNK solver on a vector
335       computer. It has the potential to even improve convergence for
336       non-vector machines, but it does change the results so it is turned
337       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
338       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
339    
340    checkpoint64e (2013/03/05)
341    o pkg/ecco and several verification experiments:
342       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
343       from ecco package, and revert to unified routine in model/src/
344       Adjust verification experiments accordingly, especially gloal_oce_llc90
345       Should conclude long-standing work by Gael to reconsile the_main_loop with
346       ECCO and will enable OpenAD's revolve loop in ECCO setup.
347  o pkg/generic_advdiff:  o pkg/generic_advdiff:
348    - implement compressible flow method for multi-dim advection (similar to    - implement compressible flow method for multi-dim advection (similar to
349      gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since      gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
# Line 30  o pkg/seaice: reorganize seaice_lsr.F to Line 370  o pkg/seaice: reorganize seaice_lsr.F to
370    - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS    - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
371    - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner    - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
372  o OpenAD support  o OpenAD support
373    Reorganize S/R call for overall time-stepping loop to facilitate     Reorganize S/R call for overall time-stepping loop to facilitate
374    OpenAD revolve loop replacement     OpenAD revolve loop replacement
375    (new S/R main_do_loop.F)     (new S/R main_do_loop.F)
376  o model/src:  o model/src:
377    - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;    - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
378    - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R    - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R

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